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Full-Length Methionine synthase from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BOL experimental model PDB 3BUL experimental model PDB 5VON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 0.2 M trimethylamine N-oxide, 0.1 M Tris-HCl, pH 8.5, 20% (w/v) Polyethylene glycol monomethylethe
Crystal Properties Matthews coefficient Solvent content 3.11 60.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.804 α = 90 b = 134.804 β = 90 c = 174.738 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 MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2013-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 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 2.75 106.64 100 0.191 0.197 0.049 0.993 12.3 15.8 42467
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 2.75 2.85 100 1.6 1.673 0.481 0.672 11.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.75 106.64 40236 2154 99.98 0.20444 0.20188 0.25258 0.2216 RANDOM 79.64
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 -0.29
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 15.985 r_long_range_B_refined 15.982 r_dihedral_angle_3_deg 15.683 r_scangle_other 11.495 r_dihedral_angle_2_deg 11.243 r_mcangle_it 11.002 r_mcangle_other 11.001 r_scbond_it 7.814 r_scbond_other 7.76 r_mcbond_it 7.725
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 15.985 r_long_range_B_refined 15.982 r_dihedral_angle_3_deg 15.683 r_scangle_other 11.495 r_dihedral_angle_2_deg 11.243 r_mcangle_it 11.002 r_mcangle_other 11.001 r_scbond_it 7.814 r_scbond_other 7.76 r_mcbond_it 7.725 r_mcbond_other 7.723 r_dihedral_angle_1_deg 6.453 r_angle_refined_deg 1.27 r_angle_other_deg 0.402 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 8754 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing