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Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.1 M sodium acetate, 0.05 M ammonium sulphate, 17% polyethyleneglycol, 15% glycerole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.75 α = 90 b = 172.85 β = 98.86 c = 190.54 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 4 mirrors 2003-12-09 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD 165 mm mirrors 2003-09-15 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4 2 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.2824 MPG/DESY, HAMBURG BW6
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 2.5 20 95.3 0.133 9.4 2.6 218403 218403
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 2.5 2.65 89.3 0.445 3.1 2.6 31920
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 SAD THROUGHOUT 2.5 20 207482 207482 10921 98.54 0.18426 0.18426 0.18179 0.1819 0.23146 0.2294 RANDOM 37.445
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] 0.78 1.12 -0.9 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.893 r_dihedral_angle_4_deg 21.059 r_dihedral_angle_3_deg 18.556 r_dihedral_angle_1_deg 5.755 r_scangle_it 2.57 r_scbond_it 1.575 r_angle_refined_deg 1.385 r_mcangle_it 1.037 r_mcbond_it 0.549 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.893 r_dihedral_angle_4_deg 21.059 r_dihedral_angle_3_deg 18.556 r_dihedral_angle_1_deg 5.755 r_scangle_it 2.57 r_scbond_it 1.575 r_angle_refined_deg 1.385 r_mcangle_it 1.037 r_mcbond_it 0.549 r_nbtor_refined 0.303 r_metal_ion_refined 0.282 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43880 Nucleic Acid Atoms Solvent Atoms 946 Heterogen Atoms 740
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XDS data scaling SHELXD phasing