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Crystal structure of BRD4 Bromodomain1 with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 4M Sodium Formate, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.737 α = 90 b = 47.703 β = 90 c = 79.537 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 PIXEL DECTRIS PILATUS 6M 2019-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
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 2.12 40.91 93 0.068 0.075 0.031 0.998 14.2 5.8 6973 41.1703465367
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 2.12 2.24 0.4288 0.4874 0.233 0.904
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6afr 2.12154661767 30.2729995796 1.35674283257 6968 343 92.8447701532 0.206512454635 0.202972728454 0.2164 0.273542606247 0.2955 46.9491075467
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.0905021063 f_angle_d 1.05712410212 f_chiral_restr 0.0580853129722 f_bond_d 0.00873626566021 f_plane_restr 0.00639984277947
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing