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X-ray structure of human REV7 in complex with Shieldin3 (residues 41-74)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 288 Protein complex was in 5 mM HEPES, pH 7.4, 100 mM NaCl, 5 mM DDT at 25 mg/mL;Reservoir solution was 0.1 M MES monohydrate, pH 6.5, 1.4 M MgSO4.6H20;Cryoprotection was done in 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.99 α = 90 b = 59.99 β = 90 c = 132.47 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r Sagittal focusing 2nd crystal 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
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 29.25 98.4 0.08271 0.08478 0.01825 0.999 40.89 22.6 19399 24.07
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 2.05 1.193 1.222 0.2621 0.847 4.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 3ABD 2 29.25 1.35 19167 1919 98.45 0.2178 0.2154 0.215 0.2386 0.2398 37.57
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 11.9345 f_angle_d 0.652 f_chiral_restr 0.0466 f_bond_d 0.0042 f_plane_restr 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1817 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing