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Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with Lewis-a
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 hanging drop 4.6 298 PEG 6000, hexanediol, pH 4.6, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.733 α = 90 b = 74.733 β = 90 c = 107.039 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2008-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 50 98.6 0.059 18.3 10.8 88663 87465
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.8 0.478 8.9 4438
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 3ASP 1.6 31.25 88663 87433 4398 98.61 0.2015 0.2015 0.2006 0.1974 0.2182 0.218 RANDOM 27.2188
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 14.256 r_dihedral_angle_3_deg 11.78 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.202 r_scbond_it 1.323 r_mcangle_it 1.076 r_angle_refined_deg 1.053 r_mcbond_it 0.572 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 14.256 r_dihedral_angle_3_deg 11.78 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.202 r_scbond_it 1.323 r_mcangle_it 1.076 r_angle_refined_deg 1.053 r_mcbond_it 0.572 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4703 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 83
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling