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Crystal Structure Analysis of TM0872, a Putative SAM-dependent Methyltransferase, Complexed with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6Y PDB ENTRY 1M6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 DROP- 50 mM NA CACODYLATE pH 6.5, 5 mM HEPES pH 7.5, 0.1 M AMMONIUM SULFATE, 9 % PEG 8000, 0.25 M NACL, 1.0 MM BME, 10 MG/ML PROTEIN. WELL- 0.1M NA CACODYLATE pH 6.5, 0.1 M AMMONIUM SULFATE, 18 % PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.96 α = 90 b = 133.96 β = 90 c = 133.96 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD MARRESEARCH 2002-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.9785 APS 5ID-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 1.9 20 99.8 0.079 29 25.7 63197 63100 -3 20.8
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) 1.9 1.97 99.9 0.386 4.65 7 6264
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1M6Y 1.9 19.97 63100 63068 3187 99.9 0.206 0.205 0.205 0.2089 0.226 0.2305 RANDOM 40.5
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 3.707 c_scbond_it 2.472 c_mcangle_it 2.059 c_mcbond_it 1.43 c_angle_d 1.2 c_improper_angle_d 0.86 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4596 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing