PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 20)

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce, N.M.Krojer, T.Bradley, A.R.Collins, P.Nowak, R.P.Talon, R.Marsden, B.D.Kelm, S.Shi, J.Deane, C.M.von Delft, F.

(2017) Nat Commun 8: 15123-15123

  • DOI: https://doi.org/10.1038/ncomms15123
  • Primary Citation of Related Structures:  
    5PB7, 5PB8, 5PB9, 5PBA, 5PBB, 5PBC, 5PBD, 5PBE, 5PBF, 5PBG, 5PBH, 5PBI, 5PBJ, 5PBK, 5PBL, 5PBM, 5PBN, 5PBO, 5PBP, 5PBQ, 5PBR, 5PBS, 5PBT, 5PBU, 5PBV, 5PBW, 5PBX, 5PBY, 5PBZ, 5PC0, 5PC1, 5PC2, 5PC3, 5PC4, 5PC5, 5PC6, 5PC7, 5PC8, 5PC9, 5PCA, 5PCB, 5PCC, 5PCD, 5PCE, 5PCF, 5PCG, 5PCH, 5PCI, 5PCJ, 5PCK

  • PubMed Abstract: 

    In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.

  • Organizational Affiliation

    Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2B138Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
GTEx:  ENSG00000123636 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.068α = 90
b = 96.563β = 90
c = 57.846γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2017-10-04
    Changes: Structure summary
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references