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Japanese encephalitis virus non-structural protein 1 C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1 M Ammonium sulphate and 0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.418 α = 90 b = 78.244 β = 90 c = 163.176 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS 6M 2015-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.1 47.3 99.8 0.103 0.045 0.998 11.5 6.3 18896 34.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 99.6 0.907 0.383 0.923 2.3 6.5
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 4oie 2.1 47.3 17944 949 99.67 0.19074 0.18875 0.1888 0.22772 0.2268 RANDOM 43.029
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] 2.55 2.69 -5.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 15.289 r_long_range_B_refined 9.558 r_long_range_B_other 9.557 r_dihedral_angle_1_deg 7.361 r_scangle_other 6.777 r_scbond_it 4.643 r_scbond_other 4.643 r_mcangle_it 4.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.839 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 15.289 r_long_range_B_refined 9.558 r_long_range_B_other 9.557 r_dihedral_angle_1_deg 7.361 r_scangle_other 6.777 r_scbond_it 4.643 r_scbond_other 4.643 r_mcangle_it 4.573 r_mcangle_other 4.57 r_mcbond_it 3.328 r_mcbond_other 3.326 r_angle_refined_deg 1.785 r_angle_other_deg 1.018 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1398 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing