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Crystal Structure of human MLH1 N-terminal domain with AMP-PNP
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 20% w/v PEG 8000
0.2 M Ca Acetate
0.1 M MES pH = 6.0
0.01 M Tris pH=8.5
0.24 M Na2 Malon
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.085 α = 90 b = 178.549 β = 93.916 c = 72.467 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 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 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 1.93 67.1 90.7 0.099 0.113 9.4 4.3 69653
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 1.93 2.12 61.9 0.997 1.121
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 1.93 67.1 69652 1466 61.744 0.2 0.199 0.2034 0.2284 0.234 34.499
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] -0.22 0.197 0.243 -0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.127 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 6.335 r_lrange_it 4.271 r_lrange_other 4.174 r_scangle_it 2.276 r_scangle_other 2.276 r_mcangle_it 2.153 r_mcangle_other 2.153 r_scbond_it 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.127 r_dihedral_angle_3_deg 12.457 r_dihedral_angle_1_deg 6.335 r_lrange_it 4.271 r_lrange_other 4.174 r_scangle_it 2.276 r_scangle_other 2.276 r_mcangle_it 2.153 r_mcangle_other 2.153 r_scbond_it 1.295 r_scbond_other 1.295 r_mcbond_it 1.249 r_mcbond_other 1.248 r_angle_refined_deg 1.138 r_angle_other_deg 0.485 r_chiral_restr_other 0.244 r_dihedral_angle_2_deg 0.198 r_symmetry_nbd_other 0.173 r_nbd_refined 0.167 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.138 r_nbd_other 0.112 r_symmetry_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.054 r_dihedral_angle_other_2_deg 0.053 r_ncsr_local_group_4 0.035 r_ncsr_local_group_2 0.034 r_ncsr_local_group_5 0.033 r_ncsr_local_group_3 0.031 r_ncsr_local_group_1 0.028 r_ncsr_local_group_6 0.026 r_ext_dist_refined_b 0.014 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10422 Nucleic Acid Atoms Solvent Atoms 843 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing