4HBW

Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazoline ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.20M K3(cit), 0.1M BTProp pH 8.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1643.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.65α = 90
b = 46.02β = 90
c = 77.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-11-03MSINGLE 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
11.68529.61000.0970.0979.14.5154021540222.2
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)
11.681.781000.5920.5921.34.32189

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 REPLACEMENTTHROUGHOUT2OSS1.6929.6153591535676799.980.17690.17690.17440.2283RANDOM20.7642
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]
1.61-0.71-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg29.497
r_dihedral_angle_3_deg13.805
r_scangle_it7.243
r_scbond_it6.206
r_dihedral_angle_1_deg5.168
r_mcangle_it3.919
r_mcbond_it2.572
r_angle_refined_deg1.575
r_angle_other_deg0.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.999
r_dihedral_angle_4_deg29.497
r_dihedral_angle_3_deg13.805
r_scangle_it7.243
r_scbond_it6.206
r_dihedral_angle_1_deg5.168
r_mcangle_it3.919
r_mcbond_it2.572
r_angle_refined_deg1.575
r_angle_other_deg0.947
r_mcbond_other0.909
r_chiral_restr0.333
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1047
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms23

Software

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