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Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P2 in complex with S-Adenosyl-L-Methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M6U PDB ENTRY 3M6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 200 mM NaCl, 12% w/v PEG8000 and 100 mM
HEPES-KOH (pH7.5), microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.956 α = 90 b = 78.316 β = 107.05 c = 108.122 γ = 90
Symmetry Space Group P 1 21 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 Slits: Variable vertical and horizontal slits 2008-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.98 NSLS X4C
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 1.82 30 97 0.082 8.5 2.8 93014
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) 1.82 1.89 86.5 0.38 2 8237
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3M6U 1.82 29.068 1.34 91762 4616 97.29 0.164 0.162 0.1556 0.194 0.1879 23.235
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] -0.422 -0.178 0.308 0.114
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.731 f_angle_d 1.038 f_chiral_restr 0.066 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7084 Nucleic Acid Atoms Solvent Atoms 1285 Heterogen Atoms 54
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling