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Crystal structure of Grouper nervous necrosis virus-like particle at 3.6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 0.2 M Sodium formate, 20% (w/v) PEG 3350, pH7.2
Crystal Properties Matthews coefficient Solvent content 3.67 66.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 477.355 α = 90 b = 422.735 β = 134.03 c = 337.893 γ = 90
Symmetry Space Group C 1 2 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 MX225HE 2012-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 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 3.6 266 98.9 7.2 3.9 549703
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 AB INITIO PHASING THROUGHOUT 3.6 263.91 549703 27556 99.25 0.2567 0.2546 0.2553 0.2968 0.2942 RANDOM 103.7458
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] -0.09 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_mcangle_it 22.371 r_dihedral_angle_3_deg 20.727 r_dihedral_angle_4_deg 17.138 r_mcbond_it 14.148 r_mcbond_other 14.148 r_dihedral_angle_1_deg 7.384 r_angle_refined_deg 1.767 r_angle_other_deg 1.062 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_mcangle_it 22.371 r_dihedral_angle_3_deg 20.727 r_dihedral_angle_4_deg 17.138 r_mcbond_it 14.148 r_mcbond_other 14.148 r_dihedral_angle_1_deg 7.384 r_angle_refined_deg 1.767 r_angle_other_deg 1.062 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 203160 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 90
Software Software Software Name Purpose HKL-2000 data processing HKL-2000 data scaling REFMAC refinement