5II2

Crystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MB4Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 3DAIEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 3HMHEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 2GRCEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 2OSSEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 2OUOEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 3D7CEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental modelPDB 3DWYEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.20M K3(cit) 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly
Crystal Properties
Matthews coefficientSolvent content
2.8757.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.52α = 90
b = 58.51β = 90
c = 138.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.52

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
12.124.186990.1270.1279.16.320237
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2195.30.36825.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTEnsemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY2.124.18619140104298.90.17620.17350.2267RANDOM28.073
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]
0.560.67-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.613
r_dihedral_angle_3_deg14.346
r_dihedral_angle_4_deg13.696
r_dihedral_angle_1_deg5.46
r_mcangle_it3.153
r_mcbond_it2.417
r_mcbond_other2.346
r_angle_refined_deg1.623
r_angle_other_deg0.999
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.613
r_dihedral_angle_3_deg14.346
r_dihedral_angle_4_deg13.696
r_dihedral_angle_1_deg5.46
r_mcangle_it3.153
r_mcbond_it2.417
r_mcbond_other2.346
r_angle_refined_deg1.623
r_angle_other_deg0.999
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1871
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms57

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction