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Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a SMARCA-BD binder
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.025~0.1 M zinc acetate, 16~26% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.558 α = 90 b = 64.558 β = 90 c = 89.083 γ = 120
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 EIGER X 16M 2020-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979183 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 3 47.4 98.4 0.132 0.17 0.105 0.992 5.3 2.3 8198
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 3.18 0.827 1.073 0.674 0.674
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 47.4 6909 364 87.47 0.2285 0.2231 0.2302 0.3381 0.3347 RANDOM 83.308
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] 2.98 1.49 2.98 -9.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.387 r_dihedral_angle_3_deg 22.988 r_dihedral_angle_4_deg 18.651 r_mcangle_it 8.863 r_dihedral_angle_1_deg 7.142 r_mcbond_it 5.479 r_mcbond_other 5.478 r_angle_refined_deg 1.406 r_angle_other_deg 1.084 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.387 r_dihedral_angle_3_deg 22.988 r_dihedral_angle_4_deg 18.651 r_mcangle_it 8.863 r_dihedral_angle_1_deg 7.142 r_mcbond_it 5.479 r_mcbond_other 5.478 r_angle_refined_deg 1.406 r_angle_other_deg 1.084 r_chiral_restr 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2832 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing