5DW2

X-ray crystal structure of human BRD4(BD1) in complex with RVX297 to 1.12 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.629830% PEG2000 MME, 0.1 M potassium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.1241.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.279α = 90
b = 44.656β = 90
c = 78.015γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirrors2011-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.125099.40.0550.0610.0268.35.450572
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1698.60.4580.5080.2160.8855.34921

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.1239.0147942256699.320.12430.12290.1513RANDOM12.472
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]
0.1-0.50.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.581
r_sphericity_free32.585
r_dihedral_angle_3_deg13.573
r_sphericity_bonded10.645
r_dihedral_angle_4_deg8.745
r_rigid_bond_restr6.538
r_dihedral_angle_1_deg5.423
r_angle_refined_deg2.679
r_mcangle_it1.717
r_mcbond_it1.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.581
r_sphericity_free32.585
r_dihedral_angle_3_deg13.573
r_sphericity_bonded10.645
r_dihedral_angle_4_deg8.745
r_rigid_bond_restr6.538
r_dihedral_angle_1_deg5.423
r_angle_refined_deg2.679
r_mcangle_it1.717
r_mcbond_it1.462
r_mcbond_other1.461
r_angle_other_deg1.374
r_chiral_restr0.149
r_bond_refined_d0.032
r_gen_planes_refined0.017
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1062
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms64

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing