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Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.01M cobalt chloride, 1.8M ammonium sulfate, 0.1M MES pH 6.5, ADDITIVE: 0.001 M S-ADENOSYLMETHIONINE (SAM), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.52 α = 90 b = 112.52 β = 90 c = 112.56 γ = 90
Symmetry Space Group P 41 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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2008-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97967 APS 23-ID-B
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 2.11 30.083 99.7 0.221 11 17.9 42096 -3 40.16
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 2.11 2.19 99.6 1.53 2
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 MAD THROUGHOUT 2.11 30.083 42037 2128 99.77 0.163 0.162 0.1746 0.175 0.1868 RANDOM 63.133
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] 0.95 0.95 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.854 r_dihedral_angle_4_deg 15.286 r_dihedral_angle_3_deg 11.287 r_dihedral_angle_1_deg 5.251 r_scangle_it 3.204 r_scbond_it 2.301 r_angle_refined_deg 1.646 r_mcangle_it 1.302 r_angle_other_deg 0.947 r_mcbond_it 0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.854 r_dihedral_angle_4_deg 15.286 r_dihedral_angle_3_deg 11.287 r_dihedral_angle_1_deg 5.251 r_scangle_it 3.204 r_scbond_it 2.301 r_angle_refined_deg 1.646 r_mcangle_it 1.302 r_angle_other_deg 0.947 r_mcbond_it 0.923 r_symmetry_vdw_refined 0.288 r_mcbond_other 0.217 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.21 r_nbd_other 0.204 r_nbtor_refined 0.187 r_symmetry_vdw_other 0.184 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.096 r_nbtor_other 0.089 r_xyhbond_nbd_other 0.043 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1912 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing