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Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 48).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model 5qa1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 30% PEG 1000, 0.1M MIB buffer
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.69 α = 90 b = 57.25 β = 90 c = 113.52 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 PILATUS 6M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.46 51.12 98 0.059 0.018 1 19.4 13.6 57993 23.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.5 94.8 3.108 0.915 0.356 0.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.46 36.35 1.33 57929 2858 97.71 0.1958 0.1946 0.1961 0.2172 0.218 35.27
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.7352 f_angle_d 0.7262 f_chiral_restr 0.0741 f_plane_restr 0.0046 f_bond_d 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2694 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling REFMAC phasing