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Crystal Structure of human MLH1 N-terminal domain I219V with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.25 293 10.00%v/v isopropanol
16.00%w/v PEG 4.000
0.10 M HEPES pH=7.25
Crystal Properties Matthews coefficient Solvent content 2.93 58.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.859 α = 90 b = 93.859 β = 90 c = 87.006 γ = 120
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 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0001 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 2.1 81.284 95 0.052 0.054 22.9 12.8 21800
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 2.1 2.25 52.4 1.877 1.956 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 2.1 81.284 21800 1505 85.39 0.219 0.217 0.2215 0.25 0.2538 66.152
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] 0.177 0.089 0.177 -0.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.112 r_dihedral_angle_3_deg 11.36 r_lrange_it 6.346 r_lrange_other 6.334 r_dihedral_angle_1_deg 6.242 r_mcangle_it 4.261 r_mcangle_other 4.26 r_scangle_it 4.201 r_scangle_other 4.199 r_mcbond_it 2.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.112 r_dihedral_angle_3_deg 11.36 r_lrange_it 6.346 r_lrange_other 6.334 r_dihedral_angle_1_deg 6.242 r_mcangle_it 4.261 r_mcangle_other 4.26 r_scangle_it 4.201 r_scangle_other 4.199 r_mcbond_it 2.634 r_mcbond_other 2.632 r_scbond_it 2.498 r_scbond_other 2.498 r_angle_refined_deg 1.049 r_angle_other_deg 0.468 r_dihedral_angle_2_deg 0.179 r_nbd_refined 0.169 r_symmetry_nbd_other 0.163 r_symmetry_nbd_refined 0.163 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.122 r_nbd_other 0.106 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.052 r_symmetry_xyhbond_nbd_refined 0.044 r_dihedral_angle_other_2_deg 0.016 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_ext_dist_refined_b 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing