8ZMB | pdb_00008zmb

Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13195


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7WJS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.7767.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.99α = 90
b = 140.99β = 90
c = 132.27γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2023-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97861SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.7937.411000.1290.1320.02712022.419901
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)
12.792.941002.8192.8810.590.76223.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7WJS2.7937.411888797699.910.20440.202470.20890.243540.2432RANDOM93.594
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]
-5.22-2.61-5.2216.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.495
r_dihedral_angle_3_deg18.252
r_long_range_B_refined12.503
r_long_range_B_other12.501
r_dihedral_angle_4_deg10.096
r_scangle_other9.861
r_mcangle_it9.032
r_mcangle_other9.032
r_scbond_it6.528
r_scbond_other6.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.495
r_dihedral_angle_3_deg18.252
r_long_range_B_refined12.503
r_long_range_B_other12.501
r_dihedral_angle_4_deg10.096
r_scangle_other9.861
r_mcangle_it9.032
r_mcangle_other9.032
r_scbond_it6.528
r_scbond_other6.365
r_mcbond_it5.929
r_mcbond_other5.909
r_dihedral_angle_1_deg5.802
r_angle_refined_deg1.398
r_angle_other_deg1.124
r_chiral_restr0.056
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2736
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing