3IU5

Crystal structure of the first bromodomain of human poly-bromodomain containing protein 1 (PB1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NXBEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OO1Ensemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OSSEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2OUOEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 2RFJEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DAIEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3D7CEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY
experimental modelPDB 3DWYEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52772.1M Na malate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2562.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.96α = 90
b = 66.96β = 90
c = 40.27γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6334.599.20.0580.05813.83.5224412226221.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.7298.20.5630.56323.33187

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEnsemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY1.6334.52225522255114799.170.170.170.1680.204RANDOM11.016
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.080.08-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.687
r_dihedral_angle_4_deg18.25
r_dihedral_angle_3_deg13.159
r_scangle_it8.664
r_scbond_it5.829
r_dihedral_angle_1_deg4.46
r_mcangle_it3.264
r_mcbond_it2.078
r_angle_refined_deg1.448
r_angle_other_deg0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.687
r_dihedral_angle_4_deg18.25
r_dihedral_angle_3_deg13.159
r_scangle_it8.664
r_scbond_it5.829
r_dihedral_angle_1_deg4.46
r_mcangle_it3.264
r_mcbond_it2.078
r_angle_refined_deg1.448
r_angle_other_deg0.939
r_mcbond_other0.633
r_chiral_restr0.088
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms960
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction