☰ Navigation Tabs
Crystal structure of S-adenosylmethionine dependent methyltransferase (NP_104914.1) from Mesorhizobium loti at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 277 NANODROP, 0.2M Mg Acetate, 20.0% PEG 3350, No Buffer pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.33 α = 90 b = 58.48 β = 90 c = 142.03 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97901 SSRL BL11-1
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 1.6 29.235 99.8 0.072 10.55 64958 -3 26.708
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 1.6 1.66 99.1 0.725 1.4
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 THROUGHOUT 1.6 29.235 64882 3289 99.85 0.173 0.171 0.1799 0.2 0.2053 RANDOM 25.803
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] -0.88 0.29 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.864 r_dihedral_angle_4_deg 13.382 r_dihedral_angle_3_deg 9.371 r_scangle_it 5.235 r_dihedral_angle_1_deg 4.112 r_scbond_it 3.84 r_mcangle_it 2.182 r_mcbond_it 1.81 r_angle_refined_deg 1.53 r_angle_other_deg 1.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.864 r_dihedral_angle_4_deg 13.382 r_dihedral_angle_3_deg 9.371 r_scangle_it 5.235 r_dihedral_angle_1_deg 4.112 r_scbond_it 3.84 r_mcangle_it 2.182 r_mcbond_it 1.81 r_angle_refined_deg 1.53 r_angle_other_deg 1.368 r_mcbond_other 0.356 r_symmetry_vdw_other 0.188 r_nbd_refined 0.177 r_nbtor_refined 0.16 r_nbd_other 0.148 r_xyhbond_nbd_refined 0.094 r_symmetry_hbond_refined 0.094 r_chiral_restr 0.093 r_nbtor_other 0.072 r_symmetry_vdw_refined 0.048 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3409 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHARP phasing SHELXD phasing