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Crystal Structure of human PMS2 N-terminal domain - APO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EA6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.25 293 2.1 M Na-K phosphate pH 6.25
0.15 M LiCl
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.711 α = 90 b = 74.927 β = 90 c = 134.929 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 16M 2019-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.25 50 98.9 0.053 0.057 23.07 8 36266
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.5 96.1 0.429 0.457 5.9 8.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.256 49.254 36132 1336 99.316 0.187 0.1856 0.1885 0.2124 0.2126 51.694
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] -14.906 26.688 -11.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.928 r_dihedral_angle_3_deg 11.917 r_dihedral_angle_1_deg 5.863 r_lrange_it 5.239 r_lrange_other 5.218 r_mcangle_it 3.284 r_mcangle_other 3.284 r_scangle_it 3.188 r_scangle_other 3.187 r_mcbond_it 1.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.928 r_dihedral_angle_3_deg 11.917 r_dihedral_angle_1_deg 5.863 r_lrange_it 5.239 r_lrange_other 5.218 r_mcangle_it 3.284 r_mcangle_other 3.284 r_scangle_it 3.188 r_scangle_other 3.187 r_mcbond_it 1.968 r_mcbond_other 1.968 r_scbond_it 1.901 r_scbond_other 1.899 r_angle_refined_deg 1.033 r_angle_other_deg 0.451 r_dihedral_angle_2_deg 0.266 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_nbd_other 0.166 r_nbd_refined 0.164 r_nbtor_refined 0.154 r_nbd_other 0.128 r_xyhbond_nbd_refined 0.093 r_symmetry_nbd_refined 0.086 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.05 r_ncsr_local_group_1 0.034 r_ext_dist_refined_b 0.005 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4660 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing