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Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor JQ1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OO1 PDB entry 2OO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% PEG 3350, 0.2M (NH4)2Hcit, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.36 α = 90 b = 38.02 β = 90 c = 85.79 γ = 90
Symmetry Space Group P 2 2 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 ADSC QUANTUM 315 2010-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.36 28.452 99.9 0.068 0.068 11.4 4.4 24205 24181 13
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 1.36 1.43 99.9 0.73 0.73 1.1 4.5 3446
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 2OO1 1.36 28.45 24200 24149 1233 99.79 0.1342 0.1342 0.1314 0.1269 0.1865 0.1825 RANDOM 16.1558
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] 0.28 -0.05 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.565 r_dihedral_angle_4_deg 24.897 r_sphericity_free 14.772 r_dihedral_angle_3_deg 12.453 r_scangle_it 8.545 r_scbond_it 6.998 r_sphericity_bonded 6.524 r_dihedral_angle_1_deg 5.529 r_mcangle_it 4.99 r_mcbond_it 3.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.565 r_dihedral_angle_4_deg 24.897 r_sphericity_free 14.772 r_dihedral_angle_3_deg 12.453 r_scangle_it 8.545 r_scbond_it 6.998 r_sphericity_bonded 6.524 r_dihedral_angle_1_deg 5.529 r_mcangle_it 4.99 r_mcbond_it 3.884 r_rigid_bond_restr 3.359 r_mcbond_other 2.344 r_angle_refined_deg 1.642 r_angle_other_deg 0.974 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 903 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 35
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction