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Crystal structure of kunjin virus ns3 helicase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 4000 10%, Na Acetate 0.2 M, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.129 α = 90 b = 38.095 β = 96.98 c = 148.113 γ = 90
Symmetry Space Group C 1 2 1
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 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 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 3.1 40 99.8 0.153 10.9 3.3 17953 17953
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) 3.1 3.27 99.8 0.609 3.2 3.4 2592
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 (All) 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 2BMF 3.1 39.75 17025 925 99.77 0.24738 0.24738 0.24316 0.2429 0.33058 0.3313 RANDOM 42.418
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] -1.88 1.37 -2.71 4.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.185 r_dihedral_angle_3_deg 18.991 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_1_deg 6.541 r_scangle_it 5.009 r_scbond_it 3.122 r_mcangle_it 2.838 r_mcbond_it 1.516 r_angle_refined_deg 0.991 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.185 r_dihedral_angle_3_deg 18.991 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_1_deg 6.541 r_scangle_it 5.009 r_scbond_it 3.122 r_mcangle_it 2.838 r_mcbond_it 1.516 r_angle_refined_deg 0.991 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.079 r_chiral_restr 0.068 r_bond_refined_d 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6398 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling