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Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.26 291 2% v/v Tacsimate, pH 5.0, 0.1 M tri-sodium citrate, pH 5.26, 11.36% w/v PEG3350, 0.1 M barium chloride dihydrate
Crystal Properties Matthews coefficient Solvent content 3.51 64.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.96 α = 90 b = 203.63 β = 90 c = 206.95 γ = 90
Symmetry Space Group P 21 21 2
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 6M 2024-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.99999 SPring-8 BL45PX
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 3.187 49.48 96.8 0.355 0.363 0.077 0.998 11.9 22.1 106916
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 3.187 3.329 96.6 1.338 1.372 0.3 0.868 20.9
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 3.19 49.48 101460 5456 82.28 0.2574 0.2559 0.2545 0.2848 0.2814 RANDOM 80.98
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] -0.66 -0.02 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.589 r_dihedral_angle_3_deg 16.422 r_dihedral_angle_4_deg 15.285 r_mcangle_it 6.62 r_dihedral_angle_1_deg 6.238 r_mcbond_it 3.817 r_mcbond_other 3.817 r_angle_refined_deg 1.504 r_angle_other_deg 1.232 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.589 r_dihedral_angle_3_deg 16.422 r_dihedral_angle_4_deg 15.285 r_mcangle_it 6.62 r_dihedral_angle_1_deg 6.238 r_mcbond_it 3.817 r_mcbond_other 3.817 r_angle_refined_deg 1.504 r_angle_other_deg 1.232 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36152 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 709
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing