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Crystal Structure of Catalytic Domain of Japanese Encephalitis Virus NS3 Helicase/Nucleoside Triphosphatase at a Resolution 1.8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 15 % ethanol, 100mM Tris-HCl pH 7.0, 4% pentaerythritol etoxylate (3/4 EO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.062 α = 90 b = 68.024 β = 116.87 c = 65.219 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 100 CCD Bruker DIP-6040 2005-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 32.41 99.87 40575 41.9
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 2BHR 1.8 32.41 40575 2154 99.87 0.20196 0.19932 0.24918 0.2935 RANDOM 40.386
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] 0.01 0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.176 r_dihedral_angle_4_deg 16.151 r_dihedral_angle_3_deg 15.446 r_dihedral_angle_1_deg 6.354 r_scangle_it 4.86 r_scbond_it 3.022 r_mcangle_it 2.128 r_angle_refined_deg 1.592 r_mcbond_it 1.269 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.176 r_dihedral_angle_4_deg 16.151 r_dihedral_angle_3_deg 15.446 r_dihedral_angle_1_deg 6.354 r_scangle_it 4.86 r_scbond_it 3.022 r_mcangle_it 2.128 r_angle_refined_deg 1.592 r_mcbond_it 1.269 r_nbtor_refined 0.314 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.21 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 3364 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing