3JVK

Crystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82933.6M Na formate, 10% glycerol, soaked with 10-times excess of histone peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.131α = 90
b = 47.03β = 90
c = 77.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.819.7199.40.06316.531265212652-3-336.367
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.999.90.4014.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2OSS1.819.71126461264668599.450.1960.20.1960.259RANDOM31.489
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]
7.22-3.78-3.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.177
r_dihedral_angle_4_deg25.132
r_dihedral_angle_3_deg15.931
r_sphericity_free14.157
r_dihedral_angle_1_deg7.153
r_scangle_it4.983
r_sphericity_bonded4.8
r_scbond_it3.752
r_mcangle_it2.517
r_rigid_bond_restr2.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.177
r_dihedral_angle_4_deg25.132
r_dihedral_angle_3_deg15.931
r_sphericity_free14.157
r_dihedral_angle_1_deg7.153
r_scangle_it4.983
r_sphericity_bonded4.8
r_scbond_it3.752
r_mcangle_it2.517
r_rigid_bond_restr2.013
r_angle_refined_deg1.957
r_mcbond_it1.78
r_angle_other_deg1.088
r_mcbond_other0.732
r_symmetry_vdw_refined0.304
r_symmetry_hbond_refined0.276
r_nbd_refined0.236
r_symmetry_vdw_other0.227
r_nbd_other0.195
r_nbtor_refined0.194
r_xyhbond_nbd_refined0.187
r_chiral_restr0.109
r_nbtor_other0.096
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1091
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms4

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
MOLREPphasing