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Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 16% PEG 8000, 5 mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.01 α = 90 b = 143.3 β = 90 c = 75.85 γ = 90
Symmetry Space Group P 21 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 MAR CCD 165 mm mirrors 2008-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.85 50 96 0.052 24.6 5.04 72827 -3 39
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 1.85 1.92 97.8 0.347 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 SAD R-FREE 1.85 29.7 70528 1165 100 0.19048 0.18965 0.25 0.23764 0.2985 RANDOM 39.766
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] 0.64 -0.25 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.888 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 15.577 r_scangle_it 6.8 r_dihedral_angle_1_deg 6.185 r_scbond_it 4.512 r_mcangle_it 1.873 r_angle_refined_deg 1.706 r_mcbond_it 1.034 r_angle_other_deg 0.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.888 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 15.577 r_scangle_it 6.8 r_dihedral_angle_1_deg 6.185 r_scbond_it 4.512 r_mcangle_it 1.873 r_angle_refined_deg 1.706 r_mcbond_it 1.034 r_angle_other_deg 0.997 r_mcbond_other 0.267 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6133 Nucleic Acid Atoms Solvent Atoms 846 Heterogen Atoms 104
Software Software Software Name Purpose MAR345dtb data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling