EMDB Validation Analysis : EMD-0129

EMD-0129 › Validation analysis

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Structure of the Macrobrachium rosenbergii Nodavirus

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
3.28 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2018-10-31
2019-12-18
Macrobrachium rosenbergii nodavirus
Fitted atomic model:
6h2b (3 chains, 3776 atoms)

Model evaluation bars:

Model Metric Evaluation bar Average value
6h2b Q-score
0.461
Atom Inclusion
0.662
CCC
0.726
SMOC
0.7

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-0129) and model-map (6h2b and EMD-0129). Validation analysis of this entry is available in the main page. Documentation for the outputs of EMDB Validation Analysis can be found on the help page.

Map parameters

Recommended contour level:
Number of grid points:
Voxel size:
Minimum value:
Maximum value:
Average value:
Standard deviation:
0.02
512 × 512 × 512
1.060 × 1.060 × 1.060 Å
-0.088
0.159
0.001
0.007
Image not available

Primary map visualisation

Projections
Volume graphs
Download: EMDB Mask Learn more EMDB Raw Map Learn more Depositor Half Map 1 Depositor Half Map 2
Provided FSC(Å)
FSC 0.143 3.28
FSC 0.5 3.69
FSC half-bit -

Map and 1 fitted model

Map with model 6h2b (Structure of the Macrobrachium rosenbergii Nodavirus)
Primary map with model views
Title
X projection

X

Y projection

Y

Z projection

Z

Map with assembled model views
Title
X projection

X

Y projection

Y

Z projection

Z

Map-model fit plots
Chain scores summary
Strudel Information
Chain:
Score range:
Symmetry Information
  • Symmetry table (Applied symmetry: I)
    • Symmetry type Symmetry fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak height
      Symmetry axis #1 C 5 +0.5255, -0.004357, +0.8508 +72 +0.566
      Symmetry axis #2 C 5 -0.5255, +0.007782, +0.8508 +72 +0.5362
      Symmetry axis #3 C 5 +0.8572, +0.515, -0.001059 +72 +0.5204
      Symmetry axis #4 C 5 +0.8451, -0.5347, +0.001059 +72 +0.5203
      Symmetry axis #5 C 5 +0.009828, +0.8509, +0.5253 +72 +0.4607
      Symmetry axis #6 C 5 +0.009828, +0.8509, -0.5253 +72 +0.4607
      Symmetry axis #7 C 3 -0.0018, -0.3572, +0.934 +120 +0.5959
      Symmetry axis #8 C 3 +0.0018, +0.3572, +0.934 +120 +0.5958
      Symmetry axis #9 C 3 -0.345, +0.9386, -4.546e-08 +120 +0.4766
      Symmetry axis #10 C 3 +0.3666, +0.9304, -5.119e-08 +120 +0.4765
      Symmetry axis #11 C 3 +0.9348, -0.0108, -0.355 +120 +0.4448
      Symmetry axis #12 C 3 +0.9348, -0.0108, +0.355 +120 +0.4448
      Symmetry axis #13 C 3 +0.5801, +0.5749, -0.577 +120 +0.3652
      Symmetry axis #14 C 3 -0.5731, +0.5783, +0.5805 +120 +0.3652
      Symmetry axis #15 C 3 +0.5801, +0.5749, +0.577 +120 +0.3624
      Symmetry axis #16 C 3 -5.154e-17, -0.3714, +0.9285 +120 +0.3972
      Symmetry axis #17 C 2 -4.357e-05, -0.003772, +1 +180 +0.9238
      Symmetry axis #18 C 2 -2.776e-16, -2.776e-16, +1 +180 +0.4813
      Symmetry axis #19 C 2 -5.551e-17, -1, -5.551e-17 +180 +0.4678
      Symmetry axis #20 C 2 +1, -2.776e-16, -2.776e-16 +180 +0.4657
      Symmetry axis #21 C 2 -0.4867, -0.8111, +0.3244 +180 +0.3131
      Symmetry axis #22 C 2 -0.4867, +0.8111, -0.3244 +180 +0.313
      Symmetry axis #23 C 2 +0.5345, +0.8018, +0.2673 +180 +0.3128
      Symmetry axis #24 C 2 +0.5345, -0.8018, -0.2673 +180 +0.3127
      Symmetry axis #25 C 2 -0.8111, -0.3244, +0.4867 +180 +0.2521
      Symmetry axis #26 C 2 -0.8111, +0.3244, -0.4867 +180 +0.252
      Symmetry axis #27 C 2 +0.8018, +0.2673, +0.5345 +180 +0.2481
      Symmetry axis #28 C 2 +0.8018, -0.2673, -0.5345 +180 +0.248
      Symmetry axis #29 C 2 +0.2673, -0.5345, -0.8018 +180 +0.2386
      Symmetry axis #30 C 2 +0.2673, +0.5345, +0.8018 +180 +0.2386
      Symmetry axis #31 C 2 -0.3244, -0.4867, +0.8111 +180 +0.2381
  • Symmetry element table
    • Symmetry element type Symmetry element fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees)
      Symmetry element #1 E 1 +1, +0, +0 +0
      Symmetry element #2 C 5 +0.5255, -0.004357, +0.8508 +72
      Symmetry element #3 C 5 +0.5255, -0.004357, +0.8508 -72
      Symmetry element #4 C 5 -0.5255, +0.007782, +0.8508 +72
      Symmetry element #5 C 5 -0.5255, +0.007782, +0.8508 -72
      Symmetry element #6 C 5 +0.8572, +0.515, -0.001059 +72
      Symmetry element #7 C 5 +0.8572, +0.515, -0.001059 -72
      Symmetry element #8 C 5 +0.8451, -0.5347, +0.001059 +72
      Symmetry element #9 C 5 +0.8451, -0.5347, +0.001059 -72
      Symmetry element #10 C 5 +0.009828, +0.8509, +0.5253 +72
      Symmetry element #11 C 5 +0.009828, +0.8509, +0.5253 -72
      Symmetry element #12 C 5 +0.009828, +0.8509, -0.5253 +72
      Symmetry element #13 C 5 +0.009828, +0.8509, -0.5253 -72
      Symmetry element #14 C 5 +0.5255, -0.004357, +0.8508 +144
      Symmetry element #15 C 5 +0.5255, -0.004357, +0.8508 -144
      Symmetry element #16 C 5 -0.5255, +0.007782, +0.8508 +144
      Symmetry element #17 C 5 -0.5255, +0.007782, +0.8508 -144
      Symmetry element #18 C 5 +0.8572, +0.515, -0.001059 +144
      Symmetry element #19 C 5 +0.8572, +0.515, -0.001059 -144
      Symmetry element #20 C 5 +0.8451, -0.5347, +0.001059 +144
      Symmetry element #21 C 5 +0.8451, -0.5347, +0.001059 -144
      Symmetry element #22 C 5 +0.009828, +0.8509, +0.5253 +144
      Symmetry element #23 C 5 +0.009828, +0.8509, +0.5253 -144
      Symmetry element #24 C 5 +0.009828, +0.8509, -0.5253 +144
      Symmetry element #25 C 5 +0.009828, +0.8509, -0.5253 -144
      Symmetry element #26 C 3 -0.0018, -0.3572, +0.934 +120
      Symmetry element #27 C 3 -0.0018, -0.3572, +0.934 -120
      Symmetry element #28 C 3 +0.0018, +0.3572, +0.934 +120
      Symmetry element #29 C 3 +0.0018, +0.3572, +0.934 -120
      Symmetry element #30 C 3 -0.345, +0.9386, -4.546e-08 +120
      Symmetry element #31 C 3 -0.345, +0.9386, -4.546e-08 -120
      Symmetry element #32 C 3 +0.3666, +0.9304, -5.119e-08 +120
      Symmetry element #33 C 3 +0.3666, +0.9304, -5.119e-08 -120
      Symmetry element #34 C 3 +0.9348, -0.0108, -0.355 +120
      Symmetry element #35 C 3 +0.9348, -0.0108, -0.355 -120
      Symmetry element #36 C 3 +0.9348, -0.0108, +0.355 +120
      Symmetry element #37 C 3 +0.9348, -0.0108, +0.355 -120
      Symmetry element #38 C 3 +0.5801, +0.5749, -0.577 +120
      Symmetry element #39 C 3 +0.5801, +0.5749, -0.577 -120
      Symmetry element #40 C 3 -0.5731, +0.5783, +0.5805 +120
      Symmetry element #41 C 3 -0.5731, +0.5783, +0.5805 -120
      Symmetry element #42 C 3 +0.5801, +0.5749, +0.577 +120
      Symmetry element #43 C 3 +0.5801, +0.5749, +0.577 -120
      Symmetry element #44 C 3 -5.154e-17, -0.3714, +0.9285 +120
      Symmetry element #45 C 3 -5.154e-17, -0.3714, +0.9285 -120
      Symmetry element #46 C 2 -4.357e-05, -0.003772, +1 +180
      Symmetry element #47 C 2 -2.776e-16, -2.776e-16, +1 +180
      Symmetry element #48 C 2 -5.551e-17, -1, -5.551e-17 +180
      Symmetry element #49 C 2 +1, -2.776e-16, -2.776e-16 +180
      Symmetry element #50 C 2 -0.4867, -0.8111, +0.3244 +180
      Symmetry element #51 C 2 -0.4867, +0.8111, -0.3244 +180
      Symmetry element #52 C 2 +0.5345, +0.8018, +0.2673 +180
      Symmetry element #53 C 2 +0.5345, -0.8018, -0.2673 +180
      Symmetry element #54 C 2 -0.8111, -0.3244, +0.4867 +180
      Symmetry element #55 C 2 -0.8111, +0.3244, -0.4867 +180
      Symmetry element #56 C 2 +0.8018, +0.2673, +0.5345 +180
      Symmetry element #57 C 2 +0.8018, -0.2673, -0.5345 +180
      Symmetry element #58 C 2 +0.2673, -0.5345, -0.8018 +180
      Symmetry element #59 C 2 +0.2673, +0.5345, +0.8018 +180
      Symmetry element #60 C 2 -0.3244, -0.4867, +0.8111 +180
  • Alternative symmetry information
    • Symmetry element type Symmetry element fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak Height
      Alternative Symmetry #1 C 2 -0.0002121, -0.01193, +0.9999 +180 +0.9233
      Alternative Symmetry #2 C 2 -0.4922, +0.814, -0.3085 +180 +0.6214
      Alternative Symmetry #3 C 3 +0.001826, +0.3572, +0.934 +120 +0.6214
      Alternative Symmetry #4 C 2 -0.4922, +0.814, +0.3085 +180 +0.6214
      Alternative Symmetry #5 C 2 +0.508, +0.8036, -0.3103 +180 +0.6214
      Alternative Symmetry #6 C 3 -0.001826, -0.3572, +0.934 +120 +0.6214
      Alternative Symmetry #7 C 2 +0.5109, +0.8025, +0.3084 +180 +0.6214
      Alternative Symmetry #8 C 5 +0.5255, -0.004376, +0.8508 +72 +0.5586
      Alternative Symmetry #9 C 5 -0.5255, +0.007763, +0.8508 +72 +0.5586
      Alternative Symmetry #10 C 5 +0.8572, +0.515, -0.001047 +72 +0.5416
      Alternative Symmetry #11 C 5 +0.845, -0.5347, +0.001047 +72 +0.5416
      Alternative Symmetry #12 C 2 +0.8131, +0.2989, -0.4995 +180 +0.4957
      Alternative Symmetry #13 C 3 -0.345, +0.9386, -2.746e-08 +120 +0.4957
      Alternative Symmetry #14 C 2 +0.8131, +0.2989, +0.4995 +180 +0.4957
      Alternative Symmetry #15 C 2 +0.806, -0.3176, +0.4995 +180 +0.4957
      Alternative Symmetry #16 C 3 +0.3666, +0.9304, -4.359e-08 +120 +0.4957
      Alternative Symmetry #17 C 2 +0.806, -0.3176, -0.4995 +180 +0.4957
      Alternative Symmetry #18 C 5 +0.009828, +0.8509, +0.5253 +72 +0.4787
      Alternative Symmetry #19 C 5 +0.009828, +0.8509, -0.5253 +72 +0.4787
      Alternative Symmetry #20 C 2 -0.3132, -0.4963, +0.8097 +180 +0.4617
      Alternative Symmetry #21 C 2 +0.3017, -0.5034, +0.8097 +180 +0.4617
      Alternative Symmetry #22 C 3 +0.9348, -0.0108, -0.355 +120 +0.4617
      Alternative Symmetry #23 C 2 -0.3017, +0.5034, +0.8097 +180 +0.4617
      Alternative Symmetry #24 C 3 +0.9348, -0.0108, +0.355 +120 +0.4617
      Alternative Symmetry #25 C 2 +0.3132, +0.4963, +0.8097 +180 +0.4617
      Alternative Symmetry #26 C 3 -0.5727, +0.5807, +0.5786 +120 +0.3683
      Alternative Symmetry #27 C 3 +0.5802, +0.5749, -0.577 +120 +0.3683
      Alternative Symmetry #28 C 3 -0.5686, +0.5845, -0.5788 +120 +0.3661
      Alternative Symmetry #29 C 3 +0.5846, +0.5686, +0.5787 +120 +0.366
      Alternative Symmetry #30 D 2 -0.0002121, -0.01193, +0.9999 +180 +0.9233
      Alternative Symmetry #31 D 2 -0.0002121, -0.01193, +0.9999 +180 +0.9233
      Alternative Symmetry #32 D 2 -0.0002121, -0.01193, +0.9999 +180 +0.9233
      Alternative Symmetry #33 D 2 -0.0002121, -0.01193, +0.9999 +180 +0.9233
      Alternative Symmetry #34 D 2 -0.4922, +0.814, -0.3085 +180 +0.6214
      Alternative Symmetry #35 D 3 +0.001826, +0.3572, +0.934 +120 +0.6214
      Alternative Symmetry #36 D 2 -0.4922, +0.814, +0.3085 +180 +0.6214
      Alternative Symmetry #37 D 3 -0.001826, -0.3572, +0.934 +120 +0.6214
      Alternative Symmetry #38 D 2 -0.4922, +0.814, -0.3085 +180 +0.6214
      Alternative Symmetry #39 D 2 -0.4922, +0.814, +0.3085 +180 +0.6214
      Alternative Symmetry #40 D 2 +0.508, +0.8036, -0.3103 +180 +0.6214
      Alternative Symmetry #41 D 2 +0.5109, +0.8025, +0.3084 +180 +0.6214
      Alternative Symmetry #42 D 2 -0.4922, +0.814, -0.3085 +180 +0.6214
      Alternative Symmetry #43 D 2 -0.4922, +0.814, +0.3085 +180 +0.6214
      Alternative Symmetry #44 D 2 +0.508, +0.8036, -0.3103 +180 +0.6214
      Alternative Symmetry #45 D 2 +0.5109, +0.8025, +0.3084 +180 +0.6214
      Alternative Symmetry #46 D 5 +0.5255, -0.004376, +0.8508 +72 +0.5586
      Alternative Symmetry #47 D 5 -0.5255, +0.007763, +0.8508 +72 +0.5586
      Alternative Symmetry #48 D 5 -0.5255, +0.007763, +0.8508 +72 +0.5586
      Alternative Symmetry #49 D 5 +0.5255, -0.004376, +0.8508 +72 +0.5586
      Alternative Symmetry #50 D 2 -0.4922, +0.814, +0.3085 +180 +0.6214
      Alternative Symmetry #51 D 2 +0.5109, +0.8025, +0.3084 +180 +0.6214
      Alternative Symmetry #52 D 2 +0.508, +0.8036, -0.3103 +180 +0.6214
      Alternative Symmetry #53 D 2 -0.4922, +0.814, -0.3085 +180 +0.6214
      Alternative Symmetry #54 D 5 +0.8572, +0.515, -0.001047 +72 +0.5416
      Alternative Symmetry #55 D 5 +0.8572, +0.515, -0.001047 +72 +0.5416
      Alternative Symmetry #56 D 5 +0.845, -0.5347, +0.001047 +72 +0.5416
      Alternative Symmetry #57 D 5 +0.845, -0.5347, +0.001047 +72 +0.5416
      Alternative Symmetry #58 D 2 +0.8131, +0.2989, -0.4995 +180 +0.4957
      Alternative Symmetry #59 D 3 -0.345, +0.9386, -2.746e-08 +120 +0.4957
      Alternative Symmetry #60 D 2 +0.806, -0.3176, +0.4995 +180 +0.4957
      Alternative Symmetry #61 D 3 +0.3666, +0.9304, -4.359e-08 +120 +0.4957
      Alternative Symmetry #62 D 2 +0.8131, +0.2989, -0.4995 +180 +0.4957
      Alternative Symmetry #63 D 2 +0.806, -0.3176, +0.4995 +180 +0.4957
      Alternative Symmetry #64 D 2 +0.8131, +0.2989, +0.4995 +180 +0.4957
      Alternative Symmetry #65 D 2 +0.806, -0.3176, -0.4995 +180 +0.4957
      Alternative Symmetry #66 D 5 +0.009828, +0.8509, +0.5253 +72 +0.4787
      Alternative Symmetry #67 D 5 +0.009828, +0.8509, +0.5253 +72 +0.4787
      Alternative Symmetry #68 D 5 +0.009828, +0.8509, -0.5253 +72 +0.4787
      Alternative Symmetry #69 D 5 +0.009828, +0.8509, -0.5253 +72 +0.4787
      Alternative Symmetry #70 D 2 +0.508, +0.8036, -0.3103 +180 +0.6214
      Alternative Symmetry #71 D 2 -0.4922, +0.814, +0.3085 +180 +0.6214
      Alternative Symmetry #72 D 2 -0.4922, +0.814, -0.3085 +180 +0.6214
      Alternative Symmetry #73 D 2 +0.5109, +0.8025, +0.3084 +180 +0.6214
      Alternative Symmetry #74 D 2 +0.3017, -0.5034, +0.8097 +180 +0.4617
      Alternative Symmetry #75 D 2 -0.3132, -0.4963, +0.8097 +180 +0.4617
      Alternative Symmetry #76 D 2 -0.3017, +0.5034, +0.8097 +180 +0.4617
      Alternative Symmetry #77 D 3 +0.9348, -0.0108, -0.355 +120 +0.4617
      Alternative Symmetry #78 D 2 +0.8131, +0.2989, +0.4995 +180 +0.4957
      Alternative Symmetry #79 D 2 +0.806, -0.3176, +0.4995 +180 +0.4957
      Alternative Symmetry #80 D 2 +0.8131, +0.2989, -0.4995 +180 +0.4957
      Alternative Symmetry #81 D 2 +0.806, -0.3176, -0.4995 +180 +0.4957
      Alternative Symmetry #82 D 2 +0.3017, -0.5034, +0.8097 +180 +0.4617
      Alternative Symmetry #83 D 2 +0.3132, +0.4963, +0.8097 +180 +0.4617
      Alternative Symmetry #84 D 2 -0.3132, -0.4963, +0.8097 +180 +0.4617
      Alternative Symmetry #85 D 2 -0.3017, +0.5034, +0.8097 +180 +0.4617