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Crystal Structure of human PMS1 N-terminal domain with ATPgammaS
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 293 2 M (NH4)2SO4
0.1 M BIS-TRIS pH:5.75
2 mM ATPgammaS
5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.655 α = 90 b = 69.732 β = 103.924 c = 102.475 γ = 90
Symmetry Space Group P 1 21 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 16M 2022-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0000 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 2.18 57.16 95 0.093 0.11 11 3.5 38021
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 2.18 2.22 99.6 1.022 1.201
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 2.18 57.16 38007 1434 94.987 0.216 0.2143 0.2184 0.2636 0.2653 44.509
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] 5.648 -0.947 -0.341 -4.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.039 r_dihedral_angle_3_deg 12.922 r_lrange_it 8.425 r_lrange_other 8.227 r_dihedral_angle_1_deg 6.479 r_scangle_it 5.185 r_scangle_other 5.056 r_mcangle_it 4.278 r_mcangle_other 4.277 r_scbond_it 3.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.039 r_dihedral_angle_3_deg 12.922 r_lrange_it 8.425 r_lrange_other 8.227 r_dihedral_angle_1_deg 6.479 r_scangle_it 5.185 r_scangle_other 5.056 r_mcangle_it 4.278 r_mcangle_other 4.277 r_scbond_it 3.132 r_scbond_other 3.007 r_mcbond_it 2.649 r_mcbond_other 2.649 r_angle_refined_deg 1.28 r_angle_other_deg 0.496 r_dihedral_angle_2_deg 0.321 r_nbd_refined 0.177 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.16 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.094 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.062 r_symmetry_nbd_refined 0.058 r_symmetry_xyhbond_nbd_other 0.052 r_dihedral_angle_other_2_deg 0.048 r_ncsr_local_group_1 0.036 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 5339 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing