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N-terminal 40kDa fragment of human PMS2 with covalent ligand NP1867
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 282 20% PEG3350, 0.2 M potassium thiocyanate and 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.292 α = 90 b = 82.292 β = 90 c = 110.801 γ = 120
Symmetry Space Group P 31 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 EIGER2 XE 16M 2021-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 41.15 100 0.08 0.08 0.018 1 19.6 20.5 29917 49
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 2.05 100 1.96 2.01 0.436 0.76 1.9 21.1
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 38.602 29881 1465 99.98 0.206 0.205 0.2117 0.2293 0.2333 48.992
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] -0.538 -0.269 -0.538 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.074 r_dihedral_angle_3_deg 15.952 r_dihedral_angle_6_deg 15.317 r_scangle_it 7.887 r_scangle_other 7.885 r_lrange_it 7.801 r_lrange_other 7.796 r_dihedral_angle_1_deg 6.239 r_scbond_it 5.795 r_scbond_other 5.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.074 r_dihedral_angle_3_deg 15.952 r_dihedral_angle_6_deg 15.317 r_scangle_it 7.887 r_scangle_other 7.885 r_lrange_it 7.801 r_lrange_other 7.796 r_dihedral_angle_1_deg 6.239 r_scbond_it 5.795 r_scbond_other 5.794 r_mcangle_other 5.713 r_mcangle_it 5.705 r_mcbond_other 4.525 r_mcbond_it 4.524 r_angle_refined_deg 1.537 r_angle_other_deg 0.53 r_nbd_other 0.258 r_symmetry_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.212 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2221 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing