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Crystal Structure of human MLH1 C-terminal domain with cyclic peptide (2S)-N-[(6S,9S,12S,15S,18S,26aR)-12-(4-aminobutyl)-18-benzyl-21-(2-carbamoylethyl)-9-(hydroxymethyl)- 15-[(4-hydroxyphenyl)methyl]-1,7,10,13,16,19,22-heptaoxo-hexacosahydropyrrolo[2,1-c]1,4,7,10,13,16,19-heptaazacyclotetracosan-6-yl]-2-[(2S)-2-acetamidopropanamido]-3-methylbutanamide
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, SITTING DROP 6.25 293 14% PEG 8K
200 mM Ca-Acetate
100 mM MES pH 6.25
Crystal Properties Matthews coefficient Solvent content 3.37 63.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.302 α = 90 b = 57.43 β = 90 c = 118.007 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 EIGER2 X 16M 2023-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.28 85.907 100 0.09 0.096 0.034 0.9946 10.905 8.4 39599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.281 2.321 100 1.412 1.515 0.539 0.5268 8.03
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.281 85.907 39596 2748 99.952 0.197 0.1953 0.2 0.2202 0.2256 Random selection 57.337
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] -0.315 1.968 -1.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 26.76 r_dihedral_angle_other_6_deg 16.173 r_dihedral_angle_6_deg 13.785 r_dihedral_angle_3_deg 13.068 r_lrange_other 7.835 r_lrange_it 7.829 r_dihedral_angle_1_deg 6.324 r_scangle_it 5.876 r_scangle_other 5.875 r_mcangle_other 4.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 26.76 r_dihedral_angle_other_6_deg 16.173 r_dihedral_angle_6_deg 13.785 r_dihedral_angle_3_deg 13.068 r_lrange_other 7.835 r_lrange_it 7.829 r_dihedral_angle_1_deg 6.324 r_scangle_it 5.876 r_scangle_other 5.875 r_mcangle_other 4.691 r_mcangle_it 4.69 r_scbond_it 3.632 r_scbond_other 3.631 r_mcbond_it 3.219 r_mcbond_other 3.215 r_angle_refined_deg 1.286 r_angle_other_deg 0.569 r_dihedral_angle_2_deg 0.342 r_nbd_refined 0.193 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.167 r_symmetry_nbd_other 0.166 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.114 r_symmetry_xyhbond_nbd_refined 0.112 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.067 r_symmetry_metal_ion_refined 0.062 r_ncsr_local_group_1 0.029 r_bond_other_d 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing