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Crystal structure of the first bromodomain of human BRD4 in complex with an isoxazolyl-benzimidazole ligand
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 NaI, 0.1M BTProp pH 8.5, 20.0% PEG 3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.052 α = 90 b = 50.755 β = 90 c = 58.661 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 2012-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54180
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 1.63 19.55 95.9 0.11 0.11 11.6 4 14916 14304 13.5
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 1.63 1.72 95.9 0.57 0.57 2 3.2 1710
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 1.635 19.55 14962 13942 702 93.18 0.2147 0.2147 0.213 0.2182 0.2458 0.2487 RANDOM 14.0045
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] -0.3 1.2 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.495 r_dihedral_angle_3_deg 14.603 r_dihedral_angle_4_deg 11.894 r_dihedral_angle_1_deg 5.311 r_angle_refined_deg 1.684 r_angle_other_deg 0.988 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.495 r_dihedral_angle_3_deg 14.603 r_dihedral_angle_4_deg 11.894 r_dihedral_angle_1_deg 5.311 r_angle_refined_deg 1.684 r_angle_other_deg 0.988 r_chiral_restr 0.095 r_bond_refined_d 0.016 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 1035 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 37
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction