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Crystal Structure of human MLH1 N-terminal domain 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 5.75 293 16 %w/v PEG 8000
0.2 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 = 59.212 α = 90 b = 179.481 β = 94.131 c = 73.351 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 2021-05-21 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 1.7 89.74 90.9 0.08 0.092 8.8 4.1 110080
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 1.7 1.92 56.8 0.701 0.792 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 1.7 89.74 110080 5509 65.492 0.196 0.1947 0.1995 0.2247 0.2285 30.376
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] -0.147 0.143 0.146 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.544 r_dihedral_angle_4_deg 18.083 r_dihedral_angle_3_deg 12.864 r_dihedral_angle_1_deg 6.514 r_lrange_it 4.919 r_lrange_other 4.792 r_scangle_it 2.785 r_scangle_other 2.785 r_mcangle_it 2.229 r_mcangle_other 2.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.544 r_dihedral_angle_4_deg 18.083 r_dihedral_angle_3_deg 12.864 r_dihedral_angle_1_deg 6.514 r_lrange_it 4.919 r_lrange_other 4.792 r_scangle_it 2.785 r_scangle_other 2.785 r_mcangle_it 2.229 r_mcangle_other 2.229 r_rigid_bond_restr 2.162 r_scbond_it 1.847 r_scbond_other 1.847 r_mcbond_it 1.367 r_angle_refined_deg 1.365 r_mcbond_other 1.363 r_angle_other_deg 1.146 r_nbd_refined 0.158 r_symmetry_nbd_other 0.151 r_nbtor_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.129 r_nbd_other 0.125 r_xyhbond_nbd_refined 0.107 r_ext_dist_refined_d 0.096 r_symmetry_nbd_refined 0.078 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.057 r_ncsr_local_group_4 0.038 r_ncsr_local_group_5 0.036 r_ncsr_local_group_1 0.032 r_ncsr_local_group_2 0.029 r_ncsr_local_group_3 0.028 r_ncsr_local_group_6 0.025 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10446 Nucleic Acid Atoms Solvent Atoms 1128 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing