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Crystal Structure of human PMS2 N-terminal domain - ATPgammaS
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 0.2 M LiCl
2.3 M Na K phosphate pH=6.25
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.677 α = 90 b = 73.91 β = 90 c = 135.873 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 2020-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999 SLS X10SA
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 2.36 50 93.7 0.094 0.101 12.4 8 20258
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 2.36 50 1.118 1.204
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 2.363 50 20257 1007 65.03 0.202 0.1998 0.1999 0.238 0.2307 59.154
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] -22.501 21.975 0.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.24 r_dihedral_angle_6_deg 10.987 r_dihedral_angle_1_deg 6.182 r_lrange_it 5.408 r_lrange_other 5.22 r_mcangle_it 3.069 r_mcangle_other 3.069 r_scangle_it 2.418 r_scangle_other 2.418 r_mcbond_it 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.24 r_dihedral_angle_6_deg 10.987 r_dihedral_angle_1_deg 6.182 r_lrange_it 5.408 r_lrange_other 5.22 r_mcangle_it 3.069 r_mcangle_other 3.069 r_scangle_it 2.418 r_scangle_other 2.418 r_mcbond_it 1.73 r_mcbond_other 1.73 r_scbond_it 1.398 r_scbond_other 1.387 r_angle_refined_deg 0.972 r_angle_other_deg 0.424 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.158 r_nbd_refined 0.156 r_nbtor_refined 0.152 r_dihedral_angle_2_deg 0.138 r_symmetry_nbd_refined 0.124 r_nbd_other 0.122 r_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.071 r_dihedral_angle_other_2_deg 0.064 r_chiral_restr 0.046 r_ncsr_local_group_1 0.035 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 81 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing