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Crystal Structure of human PMS2 N-terminal domain with AMP-PNP bound
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 0.15 M LiCl
2.10 M Na K Phosphate pH=6.25
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.407 α = 90 b = 74.68 β = 90 c = 136.112 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 2019-10-23 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 2.19 50 94 0.075 0.08 14.6 8.18 30261
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 2.19 2.36 68.7 1.396 1.485
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 2.191 50 30260 1533 76.172 0.217 0.2152 0.2144 0.2455 0.2447 55.955
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] -1.504 -4.362 5.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.614 r_dihedral_angle_3_deg 12.527 r_dihedral_angle_1_deg 5.728 r_lrange_it 4.742 r_lrange_other 4.723 r_mcangle_it 2.876 r_mcangle_other 2.876 r_scangle_it 2.306 r_scangle_other 2.306 r_mcbond_it 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.614 r_dihedral_angle_3_deg 12.527 r_dihedral_angle_1_deg 5.728 r_lrange_it 4.742 r_lrange_other 4.723 r_mcangle_it 2.876 r_mcangle_other 2.876 r_scangle_it 2.306 r_scangle_other 2.306 r_mcbond_it 1.569 r_mcbond_other 1.569 r_scbond_it 1.26 r_scbond_other 1.259 r_angle_refined_deg 1.027 r_angle_other_deg 0.446 r_chiral_restr_other 0.31 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.169 r_nbd_refined 0.163 r_nbtor_refined 0.155 r_nbd_other 0.13 r_dihedral_angle_2_deg 0.106 r_symmetry_nbd_refined 0.103 r_symmetry_nbtor_other 0.071 r_xyhbond_nbd_refined 0.066 r_chiral_restr 0.048 r_ncsr_local_group_1 0.035 r_dihedral_angle_other_2_deg 0.014 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 4798 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing