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Crystal Structure of CBX7 with compound UNC4976
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 2.5 M Ammonium Sulfate, 0.1 M BIS-Tris propane PH7.0
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.735 α = 90 b = 40.514 β = 90 c = 83.172 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 PIXEL DECTRIS EIGER X 16M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.37 50 94.9 0.069 0.075 0.029 0.994 10.4 6.5 26991
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 1.37 1.39 80.4 0.431 0.514 0.274 0.659 3.2
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 1.37 36.45 25544 1399 94.94 0.19816 0.19683 0.2046 0.22295 0.2293 RANDOM 16.316
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] -0.64 0.74 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.526 r_dihedral_angle_4_deg 19.499 r_dihedral_angle_3_deg 13.134 r_dihedral_angle_1_deg 6.397 r_long_range_B_refined 3.766 r_long_range_B_other 3.606 r_scangle_other 1.975 r_mcangle_it 1.699 r_mcangle_other 1.699 r_scbond_it 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.526 r_dihedral_angle_4_deg 19.499 r_dihedral_angle_3_deg 13.134 r_dihedral_angle_1_deg 6.397 r_long_range_B_refined 3.766 r_long_range_B_other 3.606 r_scangle_other 1.975 r_mcangle_it 1.699 r_mcangle_other 1.699 r_scbond_it 1.27 r_scbond_other 1.23 r_angle_refined_deg 1.179 r_angle_other_deg 1.175 r_mcbond_it 0.986 r_mcbond_other 0.978 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 960 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction