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Crystal Structure of human MLH1 N-terminal domain I219V with AMP-PNP
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 5.75 293 16.00 %w/v PEG 8.000
0.20 M Ca Acetate
0.10 M MES pH=5.75
Crystal Properties Matthews coefficient Solvent content 2.55 51.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.875 α = 90 b = 180.014 β = 93.663 c = 72.607 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 2021-08-21 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 2.15 72.56 91.7 0.075 0.086 11.6 4.4 42412
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 2.15 2.49 66.6 0.729 0.834 2
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 2.15 72.56 42411 1958 51.911 0.218 0.2171 0.22 0.2411 0.2455 57.047
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] 0.628 -0.06 -0.017 -0.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.959 r_dihedral_angle_3_deg 12.903 r_dihedral_angle_1_deg 6.745 r_lrange_it 6.673 r_lrange_other 6.66 r_mcangle_it 4.165 r_mcangle_other 4.165 r_scangle_it 4.099 r_scangle_other 4.099 r_mcbond_it 2.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.959 r_dihedral_angle_3_deg 12.903 r_dihedral_angle_1_deg 6.745 r_lrange_it 6.673 r_lrange_other 6.66 r_mcangle_it 4.165 r_mcangle_other 4.165 r_scangle_it 4.099 r_scangle_other 4.099 r_mcbond_it 2.517 r_mcbond_other 2.51 r_scbond_it 2.419 r_scbond_other 2.419 r_angle_refined_deg 1.18 r_angle_other_deg 0.494 r_dihedral_angle_2_deg 0.256 r_chiral_restr_other 0.192 r_symmetry_nbd_other 0.178 r_nbd_refined 0.172 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.147 r_nbd_other 0.133 r_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.056 r_ncsr_local_group_2 0.038 r_ncsr_local_group_4 0.036 r_ncsr_local_group_5 0.034 r_ncsr_local_group_3 0.03 r_dihedral_angle_other_2_deg 0.027 r_ncsr_local_group_6 0.026 r_ncsr_local_group_1 0.025 r_ext_dist_refined_b 0.013 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10381 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing