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Crystal Structure of human PMS1 N-terminal domain N309S with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 2.0 M (NH4)2SO4
0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 242.077 α = 90 b = 55.784 β = 124.071 c = 142.016 γ = 90
Symmetry Space Group C 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 EIGER2 X CdTe 16M 2024-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.86 117.64 99 0.119 0.128 8.3 7 131403
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 1.86 1.89 98.1 1.751 188.2 1.3
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 1.86 117.638 131361 6620 98.94 0.213 0.2109 0.2166 0.2427 0.2464 33.268
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] -2.688 -1.213 1.324 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.889 r_dihedral_angle_3_deg 12.078 r_dihedral_angle_1_deg 6.076 r_lrange_it 5.322 r_lrange_other 5.248 r_scangle_it 3.391 r_scangle_other 3.39 r_mcangle_it 2.789 r_mcangle_other 2.789 r_scbond_it 2.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.889 r_dihedral_angle_3_deg 12.078 r_dihedral_angle_1_deg 6.076 r_lrange_it 5.322 r_lrange_other 5.248 r_scangle_it 3.391 r_scangle_other 3.39 r_mcangle_it 2.789 r_mcangle_other 2.789 r_scbond_it 2.018 r_scbond_other 2.018 r_mcbond_it 1.705 r_mcbond_other 1.704 r_angle_refined_deg 1.194 r_angle_other_deg 0.486 r_dihedral_angle_2_deg 0.286 r_dihedral_angle_other_2_deg 0.214 r_nbd_refined 0.18 r_ext_dist_refined_b 0.173 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.158 r_nbd_other 0.158 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.128 r_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.056 r_ncsr_local_group_2 0.031 r_ncsr_local_group_1 0.029 r_ncsr_local_group_5 0.029 r_ncsr_local_group_4 0.028 r_ncsr_local_group_3 0.025 r_ncsr_local_group_6 0.024 r_xyhbond_nbd_other 0.023 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10716 Nucleic Acid Atoms Solvent Atoms 856 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PARROT phasing