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Crystal structure of BRD4(1) in complex with the inhibitor MPM6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LYW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 HEPES, Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.31 α = 90 b = 44.43 β = 90 c = 76.8 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 CCD RIGAKU SATURN 944+ 2019-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 1.92 33.56 100 0.133 0.14 0.041 0.996 12.4 11.1 10317 12.31
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 1.92 1.96 100 0.36 0.384 0.133 0.938 8.1
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 4LYW 1.92 29.05 1.37 10276 497 99.97 0.1638 0.1624 0.1646 0.189 0.1503 12.92
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 16.0745 f_angle_d 0.9834 f_chiral_restr 0.0614 f_bond_d 0.0071 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1042 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction