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Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH and GTPG
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 4.6 293 0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 30 % w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.423 α = 90 b = 80.28 β = 90 c = 84.814 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 ADSC QUANTUM 210 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
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 2.3 30 100 0.091 32.6 13.8 24920 -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 2.4 100 0.662 3.4 9.7 2426
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 30 23377 1222 99.9 0.19059 0.18763 0.1951 0.24576 0.1904 RANDOM 34.26
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] 0.48 -0.38 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.493 r_dihedral_angle_3_deg 14.704 r_dihedral_angle_4_deg 14.445 r_scangle_it 8.719 r_scbond_it 6.499 r_mcangle_it 4.975 r_dihedral_angle_1_deg 4.912 r_mcbond_it 4.299 r_angle_refined_deg 1.246 r_mcbond_other 1.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.493 r_dihedral_angle_3_deg 14.704 r_dihedral_angle_4_deg 14.445 r_scangle_it 8.719 r_scbond_it 6.499 r_mcangle_it 4.975 r_dihedral_angle_1_deg 4.912 r_mcbond_it 4.299 r_angle_refined_deg 1.246 r_mcbond_other 1.209 r_angle_other_deg 0.813 r_symmetry_vdw_other 0.255 r_nbd_refined 0.196 r_nbd_other 0.188 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.138 r_symmetry_vdw_refined 0.123 r_nbtor_other 0.083 r_chiral_restr 0.066 r_bond_refined_d 0.009 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 4164 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing