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Crystal Structure of Ribosomal RNA small subunit methyltransferase A from Rickettsia bellii Determined by Iodide SAD Phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 Wizard3/4(F6): 25% PEG-1500, 0.1M SPG Buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.38 α = 90 b = 81.33 β = 90 c = 38.49 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 RIGAKU SATURN 944+ Rigaku Varimax HF 2013-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 50 99.4 0.09 14.52 32923 32726 -3 28.575
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 2.05 92.7 0.37 3.45
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 50 32923 32726 888 99.28 0.2124 0.2124 0.2096 0.2138 0.2649 0.271 RANDOM 25.956
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] -0.89 1.86 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.485 r_dihedral_angle_4_deg 16.201 r_dihedral_angle_3_deg 13.5 r_dihedral_angle_1_deg 6.899 r_mcangle_it 1.514 r_angle_refined_deg 1.51 r_mcbond_it 0.92 r_mcbond_other 0.912 r_angle_other_deg 0.804 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.485 r_dihedral_angle_4_deg 16.201 r_dihedral_angle_3_deg 13.5 r_dihedral_angle_1_deg 6.899 r_mcangle_it 1.514 r_angle_refined_deg 1.51 r_mcbond_it 0.92 r_mcbond_other 0.912 r_angle_other_deg 0.804 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction PHENIX phasing