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Crystal structure of TehB-like SAM-dependent methyltransferase (NP_600671.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277 NANODROP, 1.0M Sodium citrate, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.33 α = 90 b = 87.398 β = 90 c = 92.429 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 collimating mirror, toroid focusing mirror 2008-01-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97978 SSRL BL9-2
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 2 29.062 99.9 0.093 0.093 6.6 3.6 28773 28.45
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 2 2.05 100 0.667 0.667 1.1 3.7 2095
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 29.062 28741 1455 99.74 0.169 0.167 0.1732 0.212 0.2157 RANDOM 25.751
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] -0.23 0.58 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.979 r_dihedral_angle_4_deg 21.126 r_dihedral_angle_3_deg 15.032 r_scangle_it 6.516 r_dihedral_angle_1_deg 6.071 r_scbond_it 4.842 r_mcangle_it 2.793 r_mcbond_it 1.872 r_angle_refined_deg 1.827 r_angle_other_deg 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.979 r_dihedral_angle_4_deg 21.126 r_dihedral_angle_3_deg 15.032 r_scangle_it 6.516 r_dihedral_angle_1_deg 6.071 r_scbond_it 4.842 r_mcangle_it 2.793 r_mcbond_it 1.872 r_angle_refined_deg 1.827 r_angle_other_deg 0.987 r_mcbond_other 0.598 r_symmetry_vdw_other 0.23 r_symmetry_vdw_refined 0.203 r_nbd_other 0.202 r_nbd_refined 0.199 r_nbtor_refined 0.174 r_chiral_restr 0.167 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.073 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2820 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction autoSHARP phasing SHELXD phasing