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Crystal structure of a sam dependent methyl-transferase type 12 family protein (eca1738) from pectobacterium atrosepticum scri1043 at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 64.4% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.949 α = 90 b = 117.949 β = 90 c = 150.532 γ = 90
Symmetry Space Group P 4 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97899 SSRL BL11-1
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 1.85 29.934 99.9 0.146 0.146 4.1 7.4 90790 20.17
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 1.85 1.9 100 0.011 1.059 0.7 7.4 6634
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 (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 1.85 29.934 90758 4551 99.85 0.15 0.15 0.149 0.158 0.183 0.1888 RANDOM 22.159
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] 0.81 0.81 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 16.011 r_dihedral_angle_3_deg 13.637 r_scangle_it 6.836 r_dihedral_angle_1_deg 5.808 r_scbond_it 4.568 r_mcangle_it 2.802 r_mcbond_it 1.714 r_angle_refined_deg 1.413 r_angle_other_deg 0.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.791 r_dihedral_angle_4_deg 16.011 r_dihedral_angle_3_deg 13.637 r_scangle_it 6.836 r_dihedral_angle_1_deg 5.808 r_scbond_it 4.568 r_mcangle_it 2.802 r_mcbond_it 1.714 r_angle_refined_deg 1.413 r_angle_other_deg 0.906 r_mcbond_other 0.692 r_symmetry_vdw_other 0.335 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.218 r_nbd_other 0.195 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.119 r_symmetry_metal_ion_refined 0.119 r_chiral_restr 0.089 r_nbtor_other 0.085 r_metal_ion_refined 0.076 r_xyhbond_nbd_other 0.067 r_bond_refined_d 0.014 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 7263 Nucleic Acid Atoms Solvent Atoms 677 Heterogen Atoms 67
Software Software Software Name Purpose MolProbity model building SOLVE phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling