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Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAM and GTPA
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 12 % w/v PEG 20000, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.021 α = 90 b = 81.021 β = 90 c = 94.011 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 315 2006-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97930 ESRF ID23-1
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 2.8 30 100 0.141 23.2 12.8 8177 -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 2.8 2.9 100 0.695 2.6 13.1 789
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 2.8 30 7732 411 99.99 0.20547 0.20263 0.2055 0.25634 0.2085 RANDOM 42.987
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] -0.68 -0.68 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.017 r_dihedral_angle_3_deg 16.074 r_dihedral_angle_4_deg 15.222 r_scangle_it 7.589 r_scbond_it 5.454 r_dihedral_angle_1_deg 4.407 r_mcangle_it 4.269 r_mcbond_it 3.29 r_angle_refined_deg 1.253 r_mcbond_other 0.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.017 r_dihedral_angle_3_deg 16.074 r_dihedral_angle_4_deg 15.222 r_scangle_it 7.589 r_scbond_it 5.454 r_dihedral_angle_1_deg 4.407 r_mcangle_it 4.269 r_mcbond_it 3.29 r_angle_refined_deg 1.253 r_mcbond_other 0.815 r_angle_other_deg 0.76 r_symmetry_hbond_refined 0.258 r_symmetry_vdw_other 0.232 r_nbd_refined 0.2 r_nbd_other 0.186 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.114 r_nbtor_other 0.084 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2086 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing