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Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and pVHL:ElonginC:ElonginB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M Bis-Tris propane, pH 8.5, 0.2 M potassium thiocyanate, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.19 α = 90 b = 58.88 β = 90.33 c = 131.08 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 EIGER2 S 9M 2023-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.11 46.4 99.2 0.06 0.065 0.026 0.999 16.8 6.1 32922
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 2.11 2.17 0.409 0.477 0.238 0.905 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.11 46.4 31408 1513 99.1 0.1875 0.1853 0.1937 0.2319 0.2331 RANDOM 44.12
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] 0.16 2.23 2.23 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.549 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 7.078 r_mcangle_it 2.751 r_mcbond_it 1.694 r_mcbond_other 1.693 r_angle_refined_deg 1.544 r_angle_other_deg 1.275 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.549 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 13.774 r_dihedral_angle_1_deg 7.078 r_mcangle_it 2.751 r_mcbond_it 1.694 r_mcbond_other 1.693 r_angle_refined_deg 1.544 r_angle_other_deg 1.275 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3741 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing