8ZM8 | pdb_00008zm8

Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13221


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2771.0 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 8.2
Crystal Properties
Matthews coefficientSolvent content
3.8868.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.067α = 90
b = 142.067β = 90
c = 134.141γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 6M2024-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97918SSRFBL02U1

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
13123.031000.1670.1720.0390.99812.418.816573
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)
133.181001.531.5710.3520.88219.6

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 REPLACEMENTTHROUGHOUT7WJS3123.031566086399.880.209620.206550.21350.264510.261RANDOM92.681
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]
-4.75-2.38-4.7515.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.399
r_dihedral_angle_3_deg19.779
r_long_range_B_other12.354
r_long_range_B_refined12.352
r_dihedral_angle_4_deg11.982
r_scangle_other8.679
r_mcangle_other8.391
r_mcangle_it8.389
r_dihedral_angle_1_deg6.351
r_mcbond_it5.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.399
r_dihedral_angle_3_deg19.779
r_long_range_B_other12.354
r_long_range_B_refined12.352
r_dihedral_angle_4_deg11.982
r_scangle_other8.679
r_mcangle_other8.391
r_mcangle_it8.389
r_dihedral_angle_1_deg6.351
r_mcbond_it5.309
r_scbond_it5.289
r_scbond_other5.289
r_mcbond_other5.284
r_angle_refined_deg1.472
r_angle_other_deg1.107
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.004
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 Atoms2732
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing