3U5J

Crystal Structure of the first bromodomain of human BRD4 in complex with Alprazolam


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.2M Na2SO4, 0.1M BTProp pH 6.5, 20% PEG3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.3α = 90
b = 44.21β = 90
c = 78.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-05-26MSINGLE 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
11.629.32298.60.0560.05620.76.3177201747214
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)
11.61.6995.30.2250.2253.45.32392

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 REPLACEMENTTHROUGHOUT2OSS1.629.32177211742989298.350.14760.14760.1460.1772RANDOM14.0742
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]
0.48-0.16-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.206
r_dihedral_angle_4_deg12.586
r_dihedral_angle_3_deg11.559
r_dihedral_angle_1_deg6.711
r_angle_refined_deg1.538
r_angle_other_deg0.924
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.206
r_dihedral_angle_4_deg12.586
r_dihedral_angle_3_deg11.559
r_dihedral_angle_1_deg6.711
r_angle_refined_deg1.538
r_angle_other_deg0.924
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1052
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms38

Software

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