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Crystal structure of BCOR/PCGF1/KDM2B complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JH5 5JH5, 4HPL experimental model PDB 4HPL 5JH5, 4HPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 293 0.1M magnesium acetate, 0.1M sodium citrate pH6.2, 4% PEG5000MME
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.291 α = 90 b = 67.291 β = 90 c = 252.035 γ = 90
Symmetry Space Group P 43 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 2021-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9793 SSRF BL19U1
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 2.2 126.02 100 0.117 0.122 0.033 0.998 12 13.8 30637
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 2.2 2.27 99.9 1.218 1.262 0.329 0.936 14.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5JH5, 4HPL 2.2 65.01 29020 1522 99.94 0.20214 0.20023 0.2052 0.2384 0.2424 RANDOM 65.831
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] 2.79 2.79 -5.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.314 r_long_range_B_other 7.177 r_long_range_B_refined 7.175 r_dihedral_angle_1_deg 6.126 r_dihedral_angle_2_deg 5.533 r_scangle_other 5.511 r_mcangle_other 3.847 r_mcangle_it 3.845 r_scbond_it 3.534 r_scbond_other 3.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.314 r_long_range_B_other 7.177 r_long_range_B_refined 7.175 r_dihedral_angle_1_deg 6.126 r_dihedral_angle_2_deg 5.533 r_scangle_other 5.511 r_mcangle_other 3.847 r_mcangle_it 3.845 r_scbond_it 3.534 r_scbond_other 3.533 r_mcbond_it 2.601 r_mcbond_other 2.589 r_angle_refined_deg 1.169 r_angle_other_deg 0.382 r_chiral_restr 0.054 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3522 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction