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Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH and 7M-GTP
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 0.2 M Sodium chloride, 0.1 M Bis-Tris pH 6.5, 25 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.579 α = 90 b = 87.445 β = 90 c = 100.914 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 MARMOSAIC 225 mm CCD mirrors 2006-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95350 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 94.2 0.126 10.2 6 29231 -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 68.4 0.472 2.3 4.1 2063
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PX2 2.2 30 27752 1460 94.17 0.16869 0.16615 0.2167 0.1694 RANDOM 35.313
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] -1.97 4.27 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.806 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_4_deg 10.719 r_scangle_it 8.454 r_scbond_it 5.485 r_dihedral_angle_1_deg 4.495 r_mcangle_it 3.984 r_mcbond_it 2.938 r_angle_refined_deg 1.379 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.806 r_dihedral_angle_3_deg 14.092 r_dihedral_angle_4_deg 10.719 r_scangle_it 8.454 r_scbond_it 5.485 r_dihedral_angle_1_deg 4.495 r_mcangle_it 3.984 r_mcbond_it 2.938 r_angle_refined_deg 1.379 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.182 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4206 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing