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Crystal Structure of BRD2(BD2)with Ligand ZB-BD-224 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2M ammonium sulfate, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.736 α = 90 b = 35.541 β = 117.627 c = 47.204 γ = 90
Symmetry Space Group C 1 2 1
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 S 6M 2019-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.98 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.29 42 98.1 0.166 0.067 0.961 98.3 5.7 5522 42.1319108441
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.474 0.221 0.9
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 2DVV 2.29994028999 41.8220433854 1.41696569125 5518 280 98.1326693936 0.202513494492 0.200194913028 0.2026 0.241899518161 0.2456 45.1096440118
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 12.4223983584 f_angle_d 1.11791760059 f_chiral_restr 0.0444877805887 f_bond_d 0.00913196726336 f_plane_restr 0.00700319076067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 906 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction Aimless data scaling PHASER phasing