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Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Pre-Catalytic State (Pre-Hcy-on)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SSC Homocystein and Folate domains, along with Cob domain, used as search models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 30% PEG 3350, 0.1 M Bis-Tris (pH 6.5), and 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.949 α = 90 b = 83.82 β = 90 c = 163.715 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 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2022-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-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 2.44 83.82 98.2 0.12 0.13 0.05 0.996 9.4 6.4 35755
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 2.44 2.54 93.7 0.617 0.679 0.276 0.88 5.7
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 2.45 81.99 33900 1790 98.07 0.16475 0.16109 0.1782 0.233 0.2343 RANDOM 70.54
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] -0.56 -0.46 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.366 r_long_range_B_other 13.267 r_long_range_B_refined 13.264 r_scangle_other 11.734 r_scbond_it 9.602 r_scbond_other 9.601 r_dihedral_angle_2_deg 9.429 r_mcangle_it 8.355 r_mcangle_other 8.354 r_dihedral_angle_1_deg 7.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.366 r_long_range_B_other 13.267 r_long_range_B_refined 13.264 r_scangle_other 11.734 r_scbond_it 9.602 r_scbond_other 9.601 r_dihedral_angle_2_deg 9.429 r_mcangle_it 8.355 r_mcangle_other 8.354 r_dihedral_angle_1_deg 7.097 r_mcbond_it 7.057 r_mcbond_other 7.053 r_angle_refined_deg 2.093 r_angle_other_deg 0.67 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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 6624 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing