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The crystal structure of Penaeus vannamei nodavirus P-domain (P212121)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.075M Magnesium chloride hexahydrate, 0.1M Sodium cacodylate 6.5, 30%(w/v) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.37 48.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.843 α = 90 b = 69.736 β = 90 c = 146.606 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 CCD RAYONIX MX300HE 2015-04-10 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) 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 1.22 30 86.9 0.112 0.128 0.059 38.6 4.5 134587
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 MOLECULAR REPLACEMENT THROUGHOUT 1.22 23.26 110940 5861 87.15 0.17695 0.17465 0.1735 0.22039 0.219 RANDOM 17.942
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] -0.19 0.05 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.349 r_dihedral_angle_4_deg 19.128 r_long_range_B_other 17.765 r_long_range_B_refined 17.284 r_dihedral_angle_3_deg 12.023 r_dihedral_angle_1_deg 7.109 r_scangle_other 3.819 r_scbond_it 2.574 r_scbond_other 2.574 r_angle_refined_deg 2.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.349 r_dihedral_angle_4_deg 19.128 r_long_range_B_other 17.765 r_long_range_B_refined 17.284 r_dihedral_angle_3_deg 12.023 r_dihedral_angle_1_deg 7.109 r_scangle_other 3.819 r_scbond_it 2.574 r_scbond_other 2.574 r_angle_refined_deg 2.137 r_mcangle_other 1.781 r_mcangle_it 1.777 r_mcbond_it 1.312 r_mcbond_other 1.303 r_angle_other_deg 1.015 r_chiral_restr 0.149 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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 3321 Nucleic Acid Atoms Solvent Atoms 1477 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing