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Crystal Structure of human PMS1 N-terminal domain 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 5.5 293 2M (NH4)2SO4: 2.0 M
0.1 M BIS-TRIS pH 5.5
2 mM ADP
5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.57 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.061 α = 90 b = 70.233 β = 103.856 c = 102.812 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 2022-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 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 49.96 99.5 0.106 0.127 9.5 3.3 39735
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 2.23 99.4 1.397 1.675 1.4
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 2.19 49.96 39297 1407 98.338 0.225 0.2233 0.2257 0.2699 0.2689 37.804
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] 3.469 -0.899 -0.088 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.359 r_dihedral_angle_3_deg 12.122 r_dihedral_angle_1_deg 5.911 r_lrange_it 4.389 r_lrange_other 4.096 r_mcangle_other 2.27 r_mcangle_it 2.269 r_scangle_other 2.251 r_scangle_it 2.245 r_mcbond_it 1.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.359 r_dihedral_angle_3_deg 12.122 r_dihedral_angle_1_deg 5.911 r_lrange_it 4.389 r_lrange_other 4.096 r_mcangle_other 2.27 r_mcangle_it 2.269 r_scangle_other 2.251 r_scangle_it 2.245 r_mcbond_it 1.294 r_mcbond_other 1.293 r_scbond_it 1.254 r_scbond_other 1.248 r_angle_refined_deg 1.053 r_angle_other_deg 0.439 r_dihedral_angle_2_deg 0.207 r_nbd_refined 0.162 r_symmetry_nbd_other 0.161 r_nbtor_refined 0.153 r_nbd_other 0.108 r_dihedral_angle_other_2_deg 0.091 r_symmetry_nbd_refined 0.085 r_xyhbond_nbd_refined 0.084 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_refined 0.062 r_chiral_restr 0.045 r_ncsr_local_group_1 0.02 r_bond_refined_d 0.004 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 5346 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing