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Crystal Structure of the Glycopeptide N-methyltransferase MtfA complexed with sinefungin
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 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.611 α = 90 b = 71.918 β = 103.82 c = 75.062 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 2.18 50 92.2 0.043 22.896 3.5 31659 41.9
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 2.18 2.26 64.1 0.29 2.4 2189
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 THROUGHOUT PDB ENTRY 3G2M 2.18 50 31620 1589 92.04 0.228 0.226 0.22 0.253 0.2411 RANDOM 50.357
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] -1.26 -0.02 1.74 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.603 r_dihedral_angle_3_deg 16.403 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_1_deg 6.317 r_scangle_it 3.017 r_scbond_it 1.892 r_angle_refined_deg 1.437 r_mcangle_it 1.427 r_mcbond_it 0.923 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.603 r_dihedral_angle_3_deg 16.403 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_1_deg 6.317 r_scangle_it 3.017 r_scbond_it 1.892 r_angle_refined_deg 1.437 r_mcangle_it 1.427 r_mcbond_it 0.923 r_nbtor_refined 0.301 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.181 r_symmetry_vdw_refined 0.154 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3621 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 54
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling