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The crystal structure of Penaeus vannamei nodavirus P-domain (P21)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 30%(w/v) Polyethylene glycol 4,000, 100mM MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.6 α = 90 b = 53.192 β = 109.38 c = 46.072 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 RAYONIX MX300HE 2015-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 0.9790 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.17 30 99.1 0.077 0.088 0.041 17.9 4.6 65509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.21 92.4 0.41 0.467 0.22 0.859 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.17 22.5 58534 2910 94.42 0.15159 0.15069 0.1502 0.16984 0.1694 RANDOM 17.767
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] -0.03 0.04 -0.17 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.076 r_dihedral_angle_4_deg 10.703 r_dihedral_angle_3_deg 9.692 r_dihedral_angle_1_deg 7.161 r_long_range_B_refined 6.264 r_long_range_B_other 5.803 r_scangle_other 4.24 r_scbond_it 2.943 r_scbond_other 2.943 r_angle_refined_deg 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.076 r_dihedral_angle_4_deg 10.703 r_dihedral_angle_3_deg 9.692 r_dihedral_angle_1_deg 7.161 r_long_range_B_refined 6.264 r_long_range_B_other 5.803 r_scangle_other 4.24 r_scbond_it 2.943 r_scbond_other 2.943 r_angle_refined_deg 2.117 r_mcangle_other 1.804 r_mcangle_it 1.799 r_mcbond_it 1.344 r_mcbond_other 1.302 r_angle_other_deg 0.896 r_chiral_restr 0.144 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1681 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing