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Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SSC Homocysteine and folate domains, and Cobalamin domain used as search models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 20% PEG 3350, 0.1 M Tris (pH 8.5), and 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.811 α = 90 b = 115.101 β = 90 c = 120.795 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 PILATUS3 6M K-B pair of biomorph mirrors for vertical and horizontal focusing, with two horizontally deflecting mirrors 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.38 120.79 98.8 0.549 0.605 0.251 0.908 3.8 5.6 39748
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.47 89.4 4.166 4.604 1.922 0.221 5.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.38 83.33 37865 2021 98.9 0.19642 0.19536 0.2249 0.21706 0.2531 RANDOM 36.218
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] -0.4 0.17 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.089 r_dihedral_angle_2_deg 11.874 r_dihedral_angle_1_deg 7.67 r_long_range_B_refined 7.444 r_long_range_B_other 7.443 r_scangle_other 3.572 r_mcangle_it 3.504 r_mcangle_other 3.503 r_scbond_it 2.433 r_scbond_other 2.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.089 r_dihedral_angle_2_deg 11.874 r_dihedral_angle_1_deg 7.67 r_long_range_B_refined 7.444 r_long_range_B_other 7.443 r_scangle_other 3.572 r_mcangle_it 3.504 r_mcangle_other 3.503 r_scbond_it 2.433 r_scbond_other 2.433 r_mcbond_it 2.351 r_mcbond_other 2.35 r_angle_refined_deg 2.076 r_angle_other_deg 0.693 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6646 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing