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The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.1M Imidazole:HCl pH 8.0,
1.0M Sodium Citrate Tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.099 α = 90 b = 89.371 β = 92.45 c = 86.526 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r 2010-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97942 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 50 99.2 0.088 8.1 4.4 111443 111443 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.53 98.8 0.425 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.5 36.5 110936 105371 5565 99.14 0.1649 0.16362 0.163 0.189 0.1864 RANDOM 12.229
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] -0.33 0.54 -0.17 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 15.315 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 5.326 r_scangle_it 3.757 r_scbond_it 2.347 r_angle_refined_deg 1.425 r_mcangle_it 1.361 r_angle_other_deg 0.905 r_mcbond_it 0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 15.315 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 5.326 r_scangle_it 3.757 r_scbond_it 2.347 r_angle_refined_deg 1.425 r_mcangle_it 1.361 r_angle_other_deg 0.905 r_mcbond_it 0.762 r_mcbond_other 0.229 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5438 Nucleic Acid Atoms Solvent Atoms 944 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building