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Crystal structure of RAD52 N-terminal domain in complex with fragment Z448237394
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298.15 0.05 M Sodium phosphate dibasic dihydrate, 5% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.51765323 51.1753311
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.866 α = 90 b = 147.204 β = 90 c = 251.295 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 9M 2023-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.921237 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 127.02 100 1 22.7 12.6 311573
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.902
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 2.1 127.02 295741 15662 99.99 0.17432 0.17231 0.1828 0.212 0.2203 RANDOM 43.694
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] -0.18 0.05 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.633 r_dihedral_angle_2_deg 12.31 r_long_range_B_refined 8.047 r_long_range_B_other 8.011 r_dihedral_angle_1_deg 6.191 r_scangle_other 4.478 r_mcangle_it 3.403 r_mcangle_other 3.403 r_scbond_it 2.763 r_scbond_other 2.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.633 r_dihedral_angle_2_deg 12.31 r_long_range_B_refined 8.047 r_long_range_B_other 8.011 r_dihedral_angle_1_deg 6.191 r_scangle_other 4.478 r_mcangle_it 3.403 r_mcangle_other 3.403 r_scbond_it 2.763 r_scbond_other 2.763 r_mcbond_it 2.067 r_mcbond_other 2.067 r_angle_refined_deg 1.66 r_angle_other_deg 0.589 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 32358 Nucleic Acid Atoms Solvent Atoms 2045 Heterogen Atoms 903
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling DIMPLE phasing