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Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Orthorhombic crystal form)
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 293 0.2 M Magnesium sulfate, 20 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.9 α = 90 b = 89.1 β = 90 c = 101.9 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 2005-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 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 2.3 30 95.9 0.123 12.3 6.2 27379 -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 2.3 2.4 81.3 0.436 2.3 4.5 2276
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 2.3 20.12 25651 1328 96.07 0.19035 0.18681 0.2011 0.2601 0.271 RANDOM 48.621
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] -0.87 1.66 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.137 r_dihedral_angle_4_deg 15.742 r_dihedral_angle_3_deg 15.419 r_scangle_it 8.974 r_scbond_it 7.214 r_mcangle_it 5.258 r_dihedral_angle_1_deg 4.868 r_mcbond_it 4.647 r_mcbond_other 1.376 r_angle_refined_deg 1.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.137 r_dihedral_angle_4_deg 15.742 r_dihedral_angle_3_deg 15.419 r_scangle_it 8.974 r_scbond_it 7.214 r_mcangle_it 5.258 r_dihedral_angle_1_deg 4.868 r_mcbond_it 4.647 r_mcbond_other 1.376 r_angle_refined_deg 1.147 r_angle_other_deg 0.84 r_symmetry_hbond_refined 0.237 r_nbd_other 0.192 r_nbd_refined 0.19 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_other 0.167 r_symmetry_vdw_refined 0.162 r_nbtor_other 0.083 r_chiral_restr 0.059 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4181 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing