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Putative RNA methyltransferase from Yersinia pestis in complex with S-ADENOSYL-L-HOMOCYSTEINE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.1 M Bis-Tris, 20 % PEG MME 5000, 10 mM S-ADENOSYL-L-HOMOCYSTEINE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.49 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.718 α = 90 b = 72.275 β = 90 c = 86.819 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2010-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
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 1.76 40.4 100 0.064 10.8 6.9 37358 37358 32.9
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) 1.76 1.79 99.9 0.764 1.99 4.5 1849
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 3N4J 1.76 40.5 37295 37295 1865 99.75 0.163 0.163 0.161 0.1656 0.193 0.2004 RANDOM 25.491
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] -0.5 -0.16 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.744 r_dihedral_angle_4_deg 20.801 r_dihedral_angle_3_deg 14.726 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.98 r_scbond_it 2.533 r_mcangle_it 1.872 r_angle_refined_deg 1.71 r_mcbond_it 1.078 r_angle_other_deg 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.744 r_dihedral_angle_4_deg 20.801 r_dihedral_angle_3_deg 14.726 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.98 r_scbond_it 2.533 r_mcangle_it 1.872 r_angle_refined_deg 1.71 r_mcbond_it 1.078 r_angle_other_deg 0.987 r_mcbond_other 0.315 r_chiral_restr 0.106 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2563 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction MOLREP phasing HKL-3000 phasing