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Japanese encephalitis virus capsid protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 18% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 16 % w/v polyethylene glycol 4,000.
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.31 α = 90 b = 49.78 β = 90 c = 68.25 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 PIXEL DECTRIS PILATUS3 S 6M 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.928 Diamond I04
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 1.98 38.32 99.6 0.058 0.44 0.999 12.1 4.5 11457 37.964
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 1.98 2.03 99 0.862 0.686 0.551 1.4 4.3
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 1sfk 1.98 38.32 10871 550 99.44 0.19026 0.18791 0.1988 0.23731 0.2567 RANDOM 43.62
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] 2.56 -2.47 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.981 r_dihedral_angle_3_deg 11.093 r_long_range_B_refined 7.956 r_long_range_B_other 7.954 r_dihedral_angle_4_deg 6.452 r_scangle_other 6.173 r_dihedral_angle_1_deg 4.697 r_scbond_it 4.092 r_scbond_other 4.084 r_mcangle_it 3.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.981 r_dihedral_angle_3_deg 11.093 r_long_range_B_refined 7.956 r_long_range_B_other 7.954 r_dihedral_angle_4_deg 6.452 r_scangle_other 6.173 r_dihedral_angle_1_deg 4.697 r_scbond_it 4.092 r_scbond_other 4.084 r_mcangle_it 3.656 r_mcangle_other 3.655 r_mcbond_other 2.749 r_mcbond_it 2.748 r_angle_refined_deg 1.428 r_angle_other_deg 0.989 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 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 1136 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing