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Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L9K PDB entry 1L9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.5mM SAH, 0.2M Calcium chloride, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.4 α = 90 b = 68.3 β = 98.4 c = 82 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 MARMOSAIC 225 mm CCD mirrors 2005-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97626 ESRF BM14
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 30 92.6 0.071 15.5 3.1 31650 -1.5
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) 2 2.07 60 0.245 2.6 1.7 2026
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1L9K 2 27.4 26662 1415 81.66 0.2039 0.20012 0.2188 0.27314 0.2853 RANDOM 34.372
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] -1.22 1.02 -2.57 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.044 r_dihedral_angle_3_deg 15.391 r_dihedral_angle_4_deg 14.905 r_scangle_it 10.153 r_scbond_it 7.933 r_mcangle_it 5.821 r_mcbond_it 5.67 r_dihedral_angle_1_deg 5.236 r_mcbond_other 1.677 r_angle_refined_deg 1.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.044 r_dihedral_angle_3_deg 15.391 r_dihedral_angle_4_deg 14.905 r_scangle_it 10.153 r_scbond_it 7.933 r_mcangle_it 5.821 r_mcbond_it 5.67 r_dihedral_angle_1_deg 5.236 r_mcbond_other 1.677 r_angle_refined_deg 1.374 r_angle_other_deg 0.851 r_symmetry_vdw_other 0.254 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.207 r_nbd_refined 0.202 r_nbd_other 0.2 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.179 r_nbtor_other 0.085 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4017 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing