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Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.09M Na HEPES pH 7.5, 1.26 Na citrate, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.46 64.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.652 α = 90 b = 79.992 β = 90.12 c = 127.068 γ = 90
Symmetry Space Group C 1 2 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 2009-02-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 ,0.97951 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 2 50 99.9 0.109 7.3 4.7 92713 92713 -3 34.6
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 2 2.03 100 0.531 4.7 4593
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 (All) 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 MAD THROUGHOUT 2 46.81 92703 92703 4638 99.4 0.162 0.162 0.16 0.1742 0.188 0.1988 RANDOM 30.564
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] -1.71 -0.45 0.28 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.743 r_dihedral_angle_4_deg 23.134 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 5.38 r_scangle_it 4.403 r_scbond_it 2.605 r_mcangle_it 1.646 r_angle_refined_deg 1.383 r_angle_other_deg 0.866 r_mcbond_it 0.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.743 r_dihedral_angle_4_deg 23.134 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 5.38 r_scangle_it 4.403 r_scbond_it 2.605 r_mcangle_it 1.646 r_angle_refined_deg 1.383 r_angle_other_deg 0.866 r_mcbond_it 0.856 r_mcbond_other 0.211 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6682 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 166
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