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Crystal Structure of the NS3 protease-helicase from Murray Valley encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8O PDB ENTRIES 2V8O, 2IJO experimental model PDB 2IJO PDB ENTRIES 2V8O, 2IJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100 MM MES PH 6.0, 20% POLYETHYLENE GLYCOL 6000, 200 MM MAGNESIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.91 α = 90 b = 105.46 β = 97.42 c = 80.068 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 293 CCD ADSC CCD MIRRORS 2007-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.75 43.937 99 0.09 19.2 7.7 17750 2
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 2.75 2.82 98 0.73 3.2 7.6
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 ENTRIES 2V8O, 2IJO 2.75 43.94 16866 884 98.6 0.268 0.267 0.2729 0.3 0.3079 RANDOM 6.17
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] -0.29 -0.24 2.68 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.945 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_4_deg 13.516 r_dihedral_angle_1_deg 4.431 r_angle_refined_deg 0.899 r_scangle_it 0.434 r_nbtor_refined 0.294 r_mcangle_it 0.267 r_scbond_it 0.246 r_symmetry_vdw_refined 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.945 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_4_deg 13.516 r_dihedral_angle_1_deg 4.431 r_angle_refined_deg 0.899 r_scangle_it 0.434 r_nbtor_refined 0.294 r_mcangle_it 0.267 r_scbond_it 0.246 r_symmetry_vdw_refined 0.173 r_nbd_refined 0.169 r_mcbond_it 0.145 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.084 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4677 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing