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Crystal structure of MLH1-CTD with CHDI-00916630
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9P4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% PEG 8K, 200 mM sodium acetate, 85 mM sodium cacodylate pH 6.5 and 12% glycerol
Crystal Properties Matthews coefficient Solvent content 2.36 47.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.62 α = 90 b = 69.47 β = 90 c = 135.17 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2022-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03322 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 34 99 0.082 0.044 0.997 9.6 4.2 43910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 99.7 1.181 0.169 0.39 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.93 33.792 43849 2148 98.766 0.174 0.1723 0.1841 0.2151 0.2258 Random selection 37.567
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] 0.234 0.62 -0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.26 r_dihedral_angle_3_deg 14.927 r_lrange_it 7.523 r_lrange_other 7.464 r_dihedral_angle_2_deg 7.222 r_dihedral_angle_1_deg 6.512 r_scangle_it 5.697 r_scangle_other 5.696 r_mcangle_it 4.106 r_mcangle_other 4.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.26 r_dihedral_angle_3_deg 14.927 r_lrange_it 7.523 r_lrange_other 7.464 r_dihedral_angle_2_deg 7.222 r_dihedral_angle_1_deg 6.512 r_scangle_it 5.697 r_scangle_other 5.696 r_mcangle_it 4.106 r_mcangle_other 4.106 r_scbond_it 3.572 r_scbond_other 3.572 r_mcbond_it 2.749 r_mcbond_other 2.741 r_angle_refined_deg 1.311 r_angle_other_deg 0.446 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.194 r_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.176 r_nbd_other 0.164 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4200 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing