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Methionine synthase from Thermus thermophilus HB8, Folate demethylation state (Fol-on)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SSC Folate and CapCob domains used as search models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293.15 1.26 M Ammonium Sulfate, 0.1M CHES-Na (pH 9.5), and 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.17 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.164 α = 90 b = 95.164 β = 90 c = 274.337 γ = 120
Symmetry Space Group P 61 2 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 MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2016-08-17 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 2.87 52.773 99.8 0.121 0.126 0.034 0.999 11.7 13.4 17680
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 2.87 3.03 98.7 2.272 2.356 0.62 0.893 14.2
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 2.87 52.77 16703 903 99.8 0.22023 0.21728 0.2143 0.27603 0.2696 RANDOM 129.406
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] 0.65 0.33 0.65 -2.11
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 25.421 r_long_range_B_other 25.421 r_scangle_other 19.563 r_dihedral_angle_3_deg 17.42 r_mcangle_it 17.274 r_mcangle_other 17.271 r_dihedral_angle_2_deg 16.357 r_scbond_it 13.303 r_scbond_other 13.3 r_mcbond_it 12.388
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 25.421 r_long_range_B_other 25.421 r_scangle_other 19.563 r_dihedral_angle_3_deg 17.42 r_mcangle_it 17.274 r_mcangle_other 17.271 r_dihedral_angle_2_deg 16.357 r_scbond_it 13.303 r_scbond_other 13.3 r_mcbond_it 12.388 r_mcbond_other 12.386 r_dihedral_angle_1_deg 7.07 r_angle_refined_deg 2.106 r_angle_other_deg 0.685 r_chiral_restr 0.164 r_bond_refined_d 0.012 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 3932 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing