☰ Navigation Tabs
Methionine synthase from Thermus thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SSC Fol and Cob domains used as search models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 25% PEG 3350, 0.1 M Tris (pH 8.5), and 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 4.21 70.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.769 α = 90 b = 187.769 β = 90 c = 325.547 γ = 90
Symmetry Space Group P 41 21 2
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 MAR CCD 300 mm K-B pair of biomorph mirrors for vertical and horizontal focusing 2015-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 3.34 325.55 99.9 0.24 0.256 0.087 0.986 6.7 8.3 85017
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 3.34 3.4 98.1 2.194 2.333 0.787 0.428 8.4
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 3.34 163.18 80679 4226 99.89 0.17783 0.17562 0.1778 0.21937 0.2175 RANDOM 118.477
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] 0.15 0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.468 r_long_range_B_other 23.468 r_scangle_other 20.114 r_mcangle_it 18.162 r_mcangle_other 18.162 r_scbond_it 14.413 r_scbond_other 14.413 r_dihedral_angle_3_deg 14.207 r_mcbond_it 12.946 r_mcbond_other 12.946
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.468 r_long_range_B_other 23.468 r_scangle_other 20.114 r_mcangle_it 18.162 r_mcangle_other 18.162 r_scbond_it 14.413 r_scbond_other 14.413 r_dihedral_angle_3_deg 14.207 r_mcbond_it 12.946 r_mcbond_other 12.946 r_dihedral_angle_2_deg 9.991 r_dihedral_angle_1_deg 5.969 r_angle_refined_deg 1.913 r_angle_other_deg 0.595 r_chiral_restr 0.078 r_bond_refined_d 0.013 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 23836 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 634
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing