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Crystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 11% PEG 8K, 0.1M CaCl2, 0.1M Hepes
Crystal Properties Matthews coefficient Solvent content 2.94 58.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.729 α = 90 b = 139.828 β = 99.99 c = 66.613 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2018-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 47.84 99.7 0.056 0.066 0.035 0.999 13.8 3.4 41672
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 0.646 0.771 0.416 0.81 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6OEB 2.2 47.84 39582 2059 99.72 0.1948 0.1936 0.2192 0.2073 RANDOM 55.49
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] -2.25 1.79 -2.67 4.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.301 r_dihedral_angle_4_deg 17.218 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_1_deg 7.301 r_angle_refined_deg 1.475 r_angle_other_deg 1.299 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.301 r_dihedral_angle_4_deg 17.218 r_dihedral_angle_3_deg 12.941 r_dihedral_angle_1_deg 7.301 r_angle_refined_deg 1.475 r_angle_other_deg 1.299 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3940 Nucleic Acid Atoms 462 Solvent Atoms 82 Heterogen Atoms 47
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing