☰ Navigation Tabs
Crystal Structure of the Glycopeptide N-methyltransferase MtfA complexed with (S)-adenosyl-L-homocysteine (SAH)
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 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.469 α = 90 b = 72.451 β = 104.19 c = 75.246 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 IMAGE PLATE RIGAKU RAXIS HTC 2007-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.95 50 97.5 0.112 12.124 3.7 13628 76.2
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 2.95 3.07 96.3 0.5 3.7 1342
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 2.95 50 13628 684 96.96 0.211 0.209 0.2077 0.259 0.2519 RANDOM 50.76
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] -2.82 -0.22 3.65 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.165 r_dihedral_angle_4_deg 20.24 r_dihedral_angle_3_deg 18.691 r_dihedral_angle_1_deg 6.728 r_scangle_it 2.226 r_angle_refined_deg 1.49 r_scbond_it 1.304 r_mcangle_it 1.089 r_mcbond_it 0.628 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.165 r_dihedral_angle_4_deg 20.24 r_dihedral_angle_3_deg 18.691 r_dihedral_angle_1_deg 6.728 r_scangle_it 2.226 r_angle_refined_deg 1.49 r_scbond_it 1.304 r_mcangle_it 1.089 r_mcbond_it 0.628 r_nbtor_refined 0.311 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.16 r_chiral_restr 0.093 r_symmetry_hbond_refined 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3703 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 45
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