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Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUL Individual domains of PDB entry 3BUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 302 0.2 M potassium nitrate, 18 % (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, temperature 302K
Crystal Properties Matthews coefficient Solvent content 3.11 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.006 α = 90 b = 107.006 β = 90 c = 141.185 γ = 90
Symmetry Space Group P 43 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 2007-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9793 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 50 100 0.043 0.085 27.3 22.4 23160 23160
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.86 99.9 0.204 0.622 5.82 22.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT Individual domains of PDB entry 3BUL 2.7 45.32 23159 23159 1130 99.9 0.246 0.246 0.2462 0.3 0.2553 RANDOM 76.7
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] -6.58 -6.58 13.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_improper_angle_d 4.32 c_scangle_it 2.98 c_mcangle_it 2.65 c_scbond_it 1.92 c_mcbond_it 1.53 c_angle_deg 1.4 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_improper_angle_d 4.32 c_scangle_it 2.98 c_mcangle_it 2.65 c_scbond_it 1.92 c_mcbond_it 1.53 c_angle_deg 1.4 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4563 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 133
Software Software Software Name Purpose Blu-Ice data collection EPMR phasing CNS refinement XDS data reduction XDS data scaling