EMD-8136 Experiments and Validation

Human core-PIC in the open state

Single particle reconstruction
Overview of EMD-8136
Sample name: Human core-PIC in the open state
Organisms: Homo sapiens, Human
Fitted atomic model: 5iyb
Related EM entries by publication: EMD-8131, EMD-8132, EMD-8133, EMD-8134, EMD-8135, EMD-8137, EMD-8138

Map parameters

Recommended contour level: 0.01 (author)
Number of grid points: 384 × 384 × 384
Voxel size: 1.31 × 1.31 × 1.31 Å
Minimum density: -0.105
Maximum density: 0.166
Average density: 0.00
Standard deviation: 0.002

Sample information

Sample name: Human core-PIC in the open state
Ligands: MAGNESIUM ION, ZINC ION
Nucleic acids: SCP-X, SCP-Y
Proteins: Human core-PIC in the open state, RNA polymerase II, General transcription factors, Super core promoter, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB2, DNA-directed RNA polymerase II subunit RPB3, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit RPB5, DNA-directed RNA polymerase II subunit RPB6, DNA-directed RNA polymerase II subunit RPB7, DNA-directed RNA polymerase II subunit RPB8, DNA-directed RNA polymerase II subunit RPB9, DNA-directed RNA polymerase II subunit RPB10, DNA-directed RNA polymerase II subunit RPB11-a, DNA-directed RNA polymerase II subunit RPB12, Transcription initiation factor IIB, Transcription initiation factor IIA subunit 1, Transcription initiation factor IIA subunit 2, TATA-box-binding protein, General transcription factor IIE subunit 1, Transcription initiation factor IIE subunit beta, General transcription factor IIF subunit 1, General transcription factor IIF subunit 2, Transcription elongation factor A protein 1

Validation information

Experimental information

 

Image processing

Software: RELION
Number of particles: 79849

Fitting

Fitting protocol: flexible

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 42.0
Nominal CS (mm): 2.70
Nominal magnification: 27500.0
Defocus max (nm): 4,000.00
Defocus min (nm): 2,000.00
Holder model: GATAN LIQUID NITROGEN

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.30
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Details: Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV)..