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Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half in a "His-On" conformation
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 7.5 302 0.2 M potassium nitrate, 20 % (w/v) PEG3350, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, temperature 302K
Crystal Properties Matthews coefficient Solvent content 3.21 61.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.55 α = 90 b = 107.55 β = 90 c = 144.8 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 IMAGE PLATE MAR scanner 300 mm plate 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 3.25 50 99.9 0.092 0.088 19.44 9.5 13886 13890
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 3.25 3.44 99.9 0.604 0.778 3.17 9.5
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 3.25 48.1 13846 13846 693 99.1 0.282 0.282 0.2759 0.321 0.3218 RANDOM 113.2
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] 2.21 2.21 -4.41
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_improper_angle_d 4.14 c_scangle_it 2.61 c_mcangle_it 2.4 c_scbond_it 1.55 c_mcbond_it 1.34 c_angle_deg 1.1 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_improper_angle_d 4.14 c_scangle_it 2.61 c_mcangle_it 2.4 c_scbond_it 1.55 c_mcbond_it 1.34 c_angle_deg 1.1 c_bond_d 0.008 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 4572 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 91
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building CNS refinement XDS data reduction XDS data scaling PHENIX phasing