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Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM SP. 255-15 at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.83 α = 116.57 b = 70.92 β = 104.63 c = 77.19 γ = 102.32
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) 2008-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 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 1.9 29.374 92.2 0.051 14.73 7.86 84662 -3 30.367
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 1.9 1.97 63.7 0.649 2.28
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 1.9 29.374 84658 4235 93.02 0.189 0.187 0.1891 0.229 0.2286 RANDOM 28.362
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] 2.03 0.45 1.72 -1.37 -0.17 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_4_deg 17.391 r_dihedral_angle_3_deg 11.583 r_scangle_it 6.083 r_scbond_it 4.681 r_dihedral_angle_1_deg 3.743 r_mcangle_it 2.546 r_mcbond_it 1.841 r_angle_refined_deg 1.587 r_angle_other_deg 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_4_deg 17.391 r_dihedral_angle_3_deg 11.583 r_scangle_it 6.083 r_scbond_it 4.681 r_dihedral_angle_1_deg 3.743 r_mcangle_it 2.546 r_mcbond_it 1.841 r_angle_refined_deg 1.587 r_angle_other_deg 0.933 r_mcbond_other 0.647 r_symmetry_vdw_other 0.297 r_nbd_refined 0.214 r_nbd_other 0.195 r_nbtor_refined 0.182 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_other 0.148 r_symmetry_hbond_refined 0.144 r_metal_ion_refined 0.103 r_chiral_restr 0.095 r_nbtor_other 0.089 r_bond_refined_d 0.015 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 7631 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction