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Crystal Structure of human MLH3 N-terminal domain C320S 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 6.5 277 0.1 M HEPES pH 6.5
0.2 M NH4Cl
19.0% w/v PEG 6.000
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.68 α = 90 b = 138.875 β = 95.502 c = 80.192 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 CdTe 16M 2024-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7749 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 2.14 79.82 94.5 0.238 0.262 4.9 5.7 50695
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.43 8.7 1.56 1.6
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 2.14 79.82 48582 2378 55.652 0.282 0.2811 0.2834 0.3006 0.3023 27.78
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] 0.663 -0.04 -0.613 -0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.955 r_dihedral_angle_6_deg 11.814 r_dihedral_angle_1_deg 6.074 r_lrange_it 3.186 r_lrange_other 3.176 r_mcangle_it 1.692 r_mcangle_other 1.692 r_angle_refined_deg 1.116 r_scangle_it 1.115 r_scangle_other 1.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.955 r_dihedral_angle_6_deg 11.814 r_dihedral_angle_1_deg 6.074 r_lrange_it 3.186 r_lrange_other 3.176 r_mcangle_it 1.692 r_mcangle_other 1.692 r_angle_refined_deg 1.116 r_scangle_it 1.115 r_scangle_other 1.115 r_mcbond_it 0.918 r_mcbond_other 0.918 r_scbond_it 0.58 r_scbond_other 0.579 r_angle_other_deg 0.484 r_chiral_restr_other 0.413 r_dihedral_angle_2_deg 0.403 r_symmetry_nbd_refined 0.207 r_nbd_other 0.192 r_symmetry_nbd_other 0.166 r_nbtor_refined 0.162 r_nbd_refined 0.161 r_dihedral_angle_other_2_deg 0.111 r_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.051 r_ncsr_local_group_1 0.051 r_ncsr_local_group_2 0.051 r_symmetry_xyhbond_nbd_refined 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11179 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing