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Crystal structure of HMCES SRAP domain in complex with longer 3' overhang DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KO9 PDB entry 5KO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 20% PEG3350, 0.1 M potassium chloride, 0.1 M Bis-Tris, 0.05 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.863 α = 90 b = 52.06 β = 93.11 c = 148.309 γ = 90
Symmetry Space Group I 1 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 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 0.977410 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 2.1 49.11 99.9 0.064 0.069 0.027 0.999 15 6.6 25066
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 2.1 2.16 99.9 0.812 0.882 0.341 0.926 6.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 5KO9 2.1 49.16 23814 1249 99.83 0.2098 0.2081 0.2179 0.242 0.2556 RANDOM 55.262
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] 3.94 -1.41 3.78 -7.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.912 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 12.468 r_dihedral_angle_1_deg 7.8 r_angle_refined_deg 1.563 r_angle_other_deg 1.303 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.912 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 12.468 r_dihedral_angle_1_deg 7.8 r_angle_refined_deg 1.563 r_angle_other_deg 1.303 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2050 Nucleic Acid Atoms 324 Solvent Atoms 46 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing