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Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+ and Homocysteine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 25% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM potasium citrate pH 4.8, 1.5% 1,2,3-heptanetriol, 10 mM YCl3. Soaking with 20% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM TRIS pH 7, 1.5% 1,2,3-heptanetriol, and 10mM Hcy , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.067 α = 90 b = 86.308 β = 100.03 c = 125.879 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 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2007-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9793 APS 23-ID-D
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 1.7 46.68 99.9 0.059 0.048 22.5 5.8 136668 136540 28.911
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) 1.7 1.8 99.9 0.323 0.399 5.36 5.8 21423
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 46.68 136668 136540 6933 99.91 0.196 0.195 0.222 0.231 RANDOM 26.688
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] 0.01 0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 18.881 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_1_deg 6.679 r_scangle_it 4.176 r_scbond_it 2.483 r_mcangle_it 1.606 r_angle_refined_deg 1.419 r_mcbond_it 0.864 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 18.881 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_1_deg 6.679 r_scangle_it 4.176 r_scbond_it 2.483 r_mcangle_it 1.606 r_angle_refined_deg 1.419 r_mcbond_it 0.864 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.1 r_metal_ion_refined 0.083 r_symmetry_metal_ion_refined 0.043 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8763 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 21
Software Software Software Name Purpose XSCALE data scaling EPMR phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction CNS refinement