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Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JVJ PDB ENTRY 3JVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.213 α = 90 b = 47.008 β = 90 c = 78.101 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 2009-11-15 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 1.75 19.6 99.7 0.086 20.1 13605 13605 -3 -3
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) 1.75 1.8 100 0.532 4.2 1072
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 (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 3JVJ 1.75 19.6 12865 12865 730 99.76 0.17451 0.17206 0.1812 0.21879 0.2278 RANDOM 29.685
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] 4.84 -2.41 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_4_deg 12.363 r_dihedral_angle_1_deg 6.144 r_scangle_it 3.7 r_scbond_it 2.781 r_angle_refined_deg 1.936 r_mcangle_it 1.79 r_mcbond_it 1.226 r_angle_other_deg 1.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_4_deg 12.363 r_dihedral_angle_1_deg 6.144 r_scangle_it 3.7 r_scbond_it 2.781 r_angle_refined_deg 1.936 r_mcangle_it 1.79 r_mcbond_it 1.226 r_angle_other_deg 1.051 r_mcbond_other 0.375 r_xyhbond_nbd_refined 0.316 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.232 r_symmetry_vdw_other 0.202 r_nbtor_refined 0.2 r_symmetry_vdw_refined 0.195 r_nbd_other 0.184 r_chiral_restr 0.116 r_nbtor_other 0.102 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1067 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing