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Crystal structure of the first bromodomain of human BRD4 with benzodiazepine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.18 M Triammonium Citrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.43 α = 82.21 b = 39.71 β = 75.25 c = 57.82 γ = 89.86
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2016-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.55 55.368 88.7 0.089 0.126 0.089 0.987 3.2 1.5 33390
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 90.2 0.531 0.751 0.531 0.601
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4Z1S 1.55 39.32 33176 1681 88.119 0.218 0.2168 0.2272 0.2462 0.2566 12.361
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] -0.658 0.002 0.489 0.283 0.302 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.355 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_4_deg 12.613 r_dihedral_angle_1_deg 5.786 r_lrange_it 3.597 r_lrange_other 3.517 r_scangle_it 2.338 r_scangle_other 2.337 r_mcangle_it 1.677 r_mcangle_other 1.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.355 r_dihedral_angle_3_deg 14.553 r_dihedral_angle_4_deg 12.613 r_dihedral_angle_1_deg 5.786 r_lrange_it 3.597 r_lrange_other 3.517 r_scangle_it 2.338 r_scangle_other 2.337 r_mcangle_it 1.677 r_mcangle_other 1.677 r_angle_refined_deg 1.594 r_scbond_it 1.503 r_scbond_other 1.502 r_angle_other_deg 1.431 r_mcbond_it 1.012 r_mcbond_other 1.012 r_nbd_refined 0.217 r_nbd_other 0.214 r_symmetry_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2090 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing