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Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P21212
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 microbatch under oil 8.5 277 160 mM Magnesium chloride hexahydrate, 80 mM TRIS-HCl (pH 8.5) and 24 % w/v
PEG4000, microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.786 α = 90 b = 109.093 β = 90 c = 50.8 γ = 90
Symmetry Space Group P 21 21 2
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 2008-10-24 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 1.68 30 99.6 0.15 5.1 6.4 110000
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) 1.68 1.74 97.8 0.487 3.9 10843
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 1.676 29.569 0.76 109375 5569 98.8 0.174 0.173 0.1698 0.192 0.1882 19.774
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] -2.319 0.326 1.993
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.41 f_angle_d 0.936 f_chiral_restr 0.061 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3557 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 1
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