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Crystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS PDB ENTRY 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 3.6M Na formate, 10% glycerol, soaked with 10-times excess of histone peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.131 α = 90 b = 47.03 β = 90 c = 77.25 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 19.71 99.4 0.063 16.53 12652 12652 -3 -3 36.367
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 99.9 0.401 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OSS 1.8 19.71 12646 12646 685 99.45 0.196 0.2 0.196 0.2064 0.259 0.2656 RANDOM 31.489
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.177 r_dihedral_angle_4_deg 25.132 r_dihedral_angle_3_deg 15.931 r_sphericity_free 14.157 r_dihedral_angle_1_deg 7.153 r_scangle_it 4.983 r_sphericity_bonded 4.8 r_scbond_it 3.752 r_mcangle_it 2.517 r_rigid_bond_restr 2.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.177 r_dihedral_angle_4_deg 25.132 r_dihedral_angle_3_deg 15.931 r_sphericity_free 14.157 r_dihedral_angle_1_deg 7.153 r_scangle_it 4.983 r_sphericity_bonded 4.8 r_scbond_it 3.752 r_mcangle_it 2.517 r_rigid_bond_restr 2.013 r_angle_refined_deg 1.957 r_mcbond_it 1.78 r_angle_other_deg 1.088 r_mcbond_other 0.732 r_symmetry_vdw_refined 0.304 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.236 r_symmetry_vdw_other 0.227 r_nbd_other 0.195 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.109 r_nbtor_other 0.096 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1091 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction MOLREP phasing