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Crystal Structure of human MLH1 N-terminal domain I219V with ADP-BeF3
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 293 16.00 %w/v PEG 8.000
0.20 M Ca Acetate
0.10 M MES pH=5.75
12 mM NaF
4 mM BeSO4
2 mM ADP
Crystal Properties Matthews coefficient Solvent content 2.58 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.067 α = 90 b = 178.784 β = 94.101 c = 73.776 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 2021-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998 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 1.74 89.392 93 0.105 0.121 8 3.9 112478
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 1.75 1.94 51.9 0.703 0.834 1.9
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 1.745 89.392 112478 2120 72.874 0.219 0.2182 0.2225 0.2577 0.2581 27.173
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] -0.348 0.084 0.435 -0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.512 r_dihedral_angle_4_deg 18.68 r_dihedral_angle_3_deg 13.332 r_dihedral_angle_1_deg 6.867 r_lrange_it 5.365 r_lrange_other 5.188 r_scangle_it 2.879 r_scangle_other 2.879 r_rigid_bond_restr 2.59 r_mcangle_it 2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.512 r_dihedral_angle_4_deg 18.68 r_dihedral_angle_3_deg 13.332 r_dihedral_angle_1_deg 6.867 r_lrange_it 5.365 r_lrange_other 5.188 r_scangle_it 2.879 r_scangle_other 2.879 r_rigid_bond_restr 2.59 r_mcangle_it 2.396 r_mcangle_other 2.396 r_scbond_it 1.768 r_scbond_other 1.768 r_mcbond_it 1.509 r_mcbond_other 1.501 r_angle_refined_deg 1.431 r_angle_other_deg 1.197 r_ext_dist_refined_d 0.46 r_nbd_refined 0.169 r_symmetry_nbd_other 0.157 r_nbtor_refined 0.141 r_nbd_other 0.127 r_symmetry_nbd_refined 0.114 r_symmetry_xyhbond_nbd_refined 0.11 r_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.064 r_ncsr_local_group_4 0.041 r_ncsr_local_group_5 0.041 r_ncsr_local_group_1 0.036 r_ncsr_local_group_3 0.034 r_ncsr_local_group_2 0.032 r_ncsr_local_group_6 0.023 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10436 Nucleic Acid Atoms Solvent Atoms 1167 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement XDS data reduction AutoProcess data scaling PHASER phasing