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Crystal Structure of the Glycopeptide N-methyltransferase MtfA complexed with (S)-adenosyl-L-methionine (SAM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G2M PDB ENTRY 3G2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 0.1M MES pH 6.5, 18% PEG-monomethyl ether 5K, vapor diffusion, hanging drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.917 α = 90 b = 72.335 β = 103.89 c = 75.306 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2007-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9798 APS 31-ID
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 2.1 50 90.8 0.04 26.008 3.5 35055 38.3
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 2.1 2.18 60.9 0.276 2.6 2346
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3G2M 2.1 42.37 35029 1783 90.58 0.218 0.216 0.2146 0.245 0.2418 RANDOM 48.143
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] -1.31 -0.49 1.99 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_4_deg 19.041 r_dihedral_angle_3_deg 15.5 r_dihedral_angle_1_deg 6.16 r_scangle_it 3.026 r_scbond_it 1.855 r_mcangle_it 1.424 r_angle_refined_deg 1.3 r_mcbond_it 0.889 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_4_deg 19.041 r_dihedral_angle_3_deg 15.5 r_dihedral_angle_1_deg 6.16 r_scangle_it 3.026 r_scbond_it 1.855 r_mcangle_it 1.424 r_angle_refined_deg 1.3 r_mcbond_it 0.889 r_nbtor_refined 0.298 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3603 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 54
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling