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Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PX2 PDB entry 2PX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.6 M Magnesium sulfate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.4 α = 90 b = 68.2 β = 115.6 c = 50.2 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 0.97650 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 2.2 30 96.5 0.091 13.8 5.2 13890 -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) 1 2.2 2.3 77.2 0.273 2.8 3.4 1109
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 2PX2 2.2 26.44 13226 676 96.39 0.16463 0.16138 0.1876 0.22927 0.247 RANDOM 32.592
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] 1.72 1.95 -0.9 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_4_deg 15.01 r_dihedral_angle_3_deg 12.273 r_scangle_it 7.276 r_scbond_it 5.505 r_dihedral_angle_1_deg 4.7 r_mcangle_it 3.701 r_mcbond_it 3.501 r_angle_refined_deg 1.037 r_mcbond_other 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_4_deg 15.01 r_dihedral_angle_3_deg 12.273 r_scangle_it 7.276 r_scbond_it 5.505 r_dihedral_angle_1_deg 4.7 r_mcangle_it 3.701 r_mcbond_it 3.501 r_angle_refined_deg 1.037 r_mcbond_other 0.896 r_angle_other_deg 0.78 r_symmetry_vdw_other 0.234 r_nbd_refined 0.183 r_nbd_other 0.182 r_symmetry_vdw_refined 0.177 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.081 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2074 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing