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Crystal structure of RAD52 N-terminal domain in complex with fragment Z271005800
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 2.51622558 51.1476288
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.874 α = 90 b = 147.194 β = 90 c = 251.155 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 2023-08-07 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) R Merge I (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 79.88 100 0.059 1 25.2 12.6 311322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.479 0.914
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 79.88 295573 15652 99.99 0.18359 0.18218 0.1926 0.21011 0.2189 RANDOM 48.996
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] 0.71 -0.18 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.522 r_dihedral_angle_2_deg 13.765 r_long_range_B_refined 8.703 r_long_range_B_other 8.703 r_scangle_other 6.69 r_dihedral_angle_1_deg 6.026 r_mcangle_it 4.888 r_mcangle_other 4.888 r_scbond_it 4.456 r_scbond_other 4.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.522 r_dihedral_angle_2_deg 13.765 r_long_range_B_refined 8.703 r_long_range_B_other 8.703 r_scangle_other 6.69 r_dihedral_angle_1_deg 6.026 r_mcangle_it 4.888 r_mcangle_other 4.888 r_scbond_it 4.456 r_scbond_other 4.455 r_mcbond_it 3.323 r_mcbond_other 3.321 r_angle_refined_deg 1.862 r_angle_other_deg 0.643 r_chiral_restr 0.088 r_bond_refined_d 0.01 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 32344 Nucleic Acid Atoms Solvent Atoms 1627 Heterogen Atoms 828
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling DIMPLE phasing