3DEM Structure-Map Validation
August 20, 2025
A new publication describes two percentile-based metrics: Q_relative_all and Q_relative_resolution. The publication presents a statistical analysis of Q-score and these new percentile based validation metrics (expanded on below).
Q_relative_all is a single value percentile, representing the overall quality of the model-map fitness. It is derived by comparing a model-map average Q-score to all model-map average Q-scores calculated for 3DEM structures in the PDB/EMDB. Higher Q_relative_all percentile values, infer higher quality in the model-map fitness.
Q_relative_resolution is a single value percentile, derived by comparing the average Q-score of a model-map with the Q-scores of other model-map entries of similar resolution. This metric was developed from the principle that average Q-score is correlated with map resolution. Q_relative_resolution percentile values close to 50% therefore represent a score that is commonly observed for entries in the PDB/EMDB of similar resolution, inferring model-map fitness is typical for an entry of a particular resolution. Notably low or high Q_relative_resolution percentiles may be helpful to guide further review of model-maps.
The EMDB has made these metrics available since Spring 2024 via emdatabank.org and since the publication of the paper, the wwPDB is in the process of incorporating these metrics into wwPDB validation reports by providing the Q-score percentile slider for the assessment of model-map fitness of 3DEM entries. This validation enhancement will help depositors, reviewers and the community to improve the quality of data submissions and assist users to assess 3DEM data quality in the PDB and EMDB, wwPDB core archives.
Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps
Grigore Pintilie, Chenghua Shao, Zhe Wang, Brian P Hudson, Justin W Flatt, Michael F Schmid, Kyle L Morris, Stephen K Burley, Wah Chiu. (2025) Acta Cryst D81: 410-422 doi: 10.1107/S2059798325005923
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RNA polymerase II bound to Gdown1 and RPAP2 (Gdown1 N-terminus map)
Cryo-EM structure of human histone deacetylase 6 tandem catalytic domain (HDAC6 CD1-2)
BC-BCCP/CT-BCCP domain of Mycobacterium tuberculosis Pyruvate carboxylase- local refinement
RNA polymerase II bound to Gdown1 and RPAP2 (Gdown1 C-terminus map)
Characterization standard for in-situ cryo-electron tomography: structure of PP7 virus-like-particle in E. coli from plunge freezing (partial dataset)
Characterization standard for in-situ cryo-electron tomography: structure of PP7 virus-like-particle in E. coli from high-pressure freezing and FIB-milling (full dataset)
Characterization standard for in-situ cryo-electron tomography: structure of PP7 virus-like-particle in E. coli from plunge freezing (full dataset)
Characterization standard for in-situ cryo-electron tomography: structure of PP7 virus-like-particle in E. coli from high-pressure freezing and FIB-milling (partial dataset)
R0-state of wild type human mitochondrial LONP1 protease bound to endogenous ADP
Locally refined cryo-EM structure of human cannabinoid receptor 2 with agonist '5249
Cryo-EM structure of human cannabinoid receptor 2-Gi complex with agonist '1029
Cryo-EM structure of human cannabinoid receptor 2-Gi complex with agonist '5249
Consensus map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S
Focused map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S
In situ structure of mouse urate oxidase assembly with helical symmetry applied
Foucused_map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)
Consensus map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)
Consensus map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S and initiator tRNA
Focused map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S (focused on tRNA-like structure)
Focused map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S and initiator tRNA
Cryo-EM structure of ATTRA97S amyloid fibrils extracted from patient-derived abdominal adipose biopsy tissue.
Focused map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S (focused on 40S head)
cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S
cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S and initiator tRNA
Consensus map for cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 80S
cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S
cryoEM structure of tobacco mosaic virus tRNA-like structure complexed with tobacco 60S and cycloheximide (CHX)
Cryo-EM structure of Congo Red-bound ATTRA97S amyloid fibrils extracted from patient-derived abdominal adipose biopsy tissu
Cryo-EM structure of ThS-bound ATTRA97S amyloid fibrils extracted from patient-derived abdominal adipose biopsy tissue.
Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P- and (partial) E/E-tRNAs
Cryo-EM structure of the LB_DQB0303_A Fab - HLA-DQB1*03:03/DQA1*02:01 human alloantibody-HLA complex
Cryo-EM structure of the LB_DQB0602_B Fab - HLA-DQB1*06:02/DQA1*01:02 human alloantibody-HLA complex
Cryo-EM composite structure of 70S ribosome of marine cold bacterium Pseudoalteromonas translucida (P. haloplanktis)TAC125.
Cryo-EM structure of the LB_DQB0301_A Fab - HLA-DQB1*03:01/DQA1*05:02 human alloantibody-HLA complex
Salmonella Flagellar Export Gate with FlhB in the context of the intact basal body
Salmonella Flagellar Export Apparatus (FliPQR/FlhB/FlhA) in the context of the intact basal body
Salmonella Flagellar Export Apparatus FlhA transmembrane domain nonamer in the context of the intact basal body
Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to target RNA with complementary PFS
Cryo-EM structure of ternary complex NSD2-PWWP1:CRBN:DDB1 in complex with NSD2-LDD, an LDD degrader
Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to target RNA with non-complementary PFS
Focused refinement map of hM4Di(GRANPA) in complex with mGsI and diphenhydramine
Latent-state loperamide-mu opioid receptor-Gi GDPbS complex (rebound) - Consensus map
Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA
Cryo-EM structure of the monomeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
Cryo-EM structure of the dimeric HIV-2 Vif-human APOBEC3H-CBFbeta complex
CryoEM structure of Gluconacetobacter diazotrophicus MoFeP (C2 symmetry)
CryoEM structure of heterologous nitrogenase complex (2:1 G. diazotrophicus-FeP:A. vinelandii-MoFeP) inhibited by BeFx (C2 symmetry)
CryoEM structure of Gluconacetobacter diazotrophicus nitrogenase complex (2:1 FeP:MoFeP) inhibited by BeFx (C2 symmetry)
CryoEM structure of Heterologous nitrogenase complex (2:1 A. vinelandii-FeP:G. diazotrophicus-MoFeP) inhibited by BeFx (C2 symmetry)
asymmetric unit of bacteriophage LUZ19 head computed in I4 symmetry
portal - core interface of bacteriophage LUZ19 computed in C4 symmetry
Portal and adaptor protein of bacteriophage LUZ19 computed in C12 symmetry
middle core protein of bacteriophage LUZ19 computed in C8 symmetry
cap and middle core protein of bacteriophage LUZ19 computed in C4 symmetry