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Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolinone ligand (RVX-208)
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 7.5 277 0.2M Na2SO4, 20% PEG3350
10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.571 α = 90 b = 44.393 β = 90 c = 78.502 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 2012-06-12 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 1.66 19.33 98.2 0.09 0.09 13.4 4.5 16062 15773 12.1
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 1.66 1.75 91.9 0.451 0.451 3 4 2104
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2OSS 1.66 19.33 16062 15734 784 97.96 0.1564 0.1544 0.1944 0.1782 RANDOM 13.608
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] 0.22 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.675 r_dihedral_angle_4_deg 18.524 r_dihedral_angle_3_deg 11.333 r_dihedral_angle_1_deg 5.614 r_angle_refined_deg 1.629 r_angle_other_deg 1.015 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.675 r_dihedral_angle_4_deg 18.524 r_dihedral_angle_3_deg 11.333 r_dihedral_angle_1_deg 5.614 r_angle_refined_deg 1.629 r_angle_other_deg 1.015 r_chiral_restr 0.107 r_bond_refined_d 0.016 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 1058 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 39
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction