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Crystal structure of P domain from norovirus GI.4 capsid protein.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ASP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293.15 0.1M tri-Sodium citrate (pH5.6), 20%(v/v) 2-Propanol , 20%(w/v) Polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.673 α = 91.74 b = 62.791 β = 97.71 c = 92.756 γ = 119.07
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD 2016-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.89 49.8 95.9 0.097 0.128 0.99 6.98 2.31 90970 20.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 2.01 94.2 0.551 0.731 0.849 1.54 2.29
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 1.89 49.8 87674 4600 96.18 0.2342 0.2321 0.2365 0.2754 0.2778 RANDOM 26.205
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] 0.02 -0.02 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.5 r_dihedral_angle_4_deg 18.05 r_dihedral_angle_3_deg 14.715 r_dihedral_angle_1_deg 8.298 r_mcangle_it 3.295 r_angle_other_deg 2.336 r_mcbond_it 2.109 r_mcbond_other 2.108 r_angle_refined_deg 1.549 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.5 r_dihedral_angle_4_deg 18.05 r_dihedral_angle_3_deg 14.715 r_dihedral_angle_1_deg 8.298 r_mcangle_it 3.295 r_angle_other_deg 2.336 r_mcbond_it 2.109 r_mcbond_other 2.108 r_angle_refined_deg 1.549 r_chiral_restr 0.066 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9138 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing