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T=1 subviral particle of Grouper nervous necrosis virus capsid protein deletion mutant (delta 1-34 & 218-338)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1M NaCl, 0.1M Lithium sulfate, 0.1M MES, pH 6.5, 30% (w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 288.947 α = 90 b = 288.947 β = 90 c = 175.124 γ = 90
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 2014-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A 1.0 NSRRC BL15A
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 3.1 30 98.3 255496 255496
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 96.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4WIZ 3.1 26.37 255496 242663 12823 98.13 0.24064 0.24064 0.23815 0.2382 0.28825 0.2851 RANDOM 55.062
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] 0.25 0.25 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.007 r_dihedral_angle_3_deg 25.076 r_dihedral_angle_4_deg 20.795 r_long_range_B_refined 11.5 r_long_range_B_other 11.5 r_dihedral_angle_1_deg 8.127 r_scangle_other 6.496 r_mcangle_it 6.43 r_mcangle_other 6.43 r_scbond_it 3.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.007 r_dihedral_angle_3_deg 25.076 r_dihedral_angle_4_deg 20.795 r_long_range_B_refined 11.5 r_long_range_B_other 11.5 r_dihedral_angle_1_deg 8.127 r_scangle_other 6.496 r_mcangle_it 6.43 r_mcangle_other 6.43 r_scbond_it 3.826 r_scbond_other 3.826 r_mcbond_it 3.743 r_mcbond_other 3.743 r_angle_refined_deg 1.59 r_angle_other_deg 0.928 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 75180 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling