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Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolinone ligand (RVX-OH)
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, SITTING DROP 8.5 277 0.2M NaBr, 0.1M BTProp, 20.0% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.74 α = 90 b = 51.972 β = 90 c = 57.539 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 IMAGE PLATE RIGAKU RAXIS IV 2013-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.52
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.68 19.37 96.7 0.032 0.032 35.4 5.4 14755 14268 12.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.77 96.7 0.101 0.101 13.9 5.2 1928
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 2OSS 1.68 19.37 14803 14232 728 96.14 0.142 0.1398 0.1534 0.1846 0.2046 RANDOM 14.0367
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] 0.14 -0.21 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_3_deg 13.035 r_dihedral_angle_1_deg 5.332 r_mcangle_it 3.844 r_mcbond_it 2.963 r_mcbond_other 2.96 r_angle_refined_deg 1.571 r_angle_other_deg 0.847 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.632 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_3_deg 13.035 r_dihedral_angle_1_deg 5.332 r_mcangle_it 3.844 r_mcbond_it 2.963 r_mcbond_other 2.96 r_angle_refined_deg 1.571 r_angle_other_deg 0.847 r_chiral_restr 0.089 r_bond_refined_d 0.013 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 1050 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction