☰ Navigation Tabs
Crystal Structure of Murine Norovirus Protruding (P) Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OBR PDB ENTRY 2OBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 20% PEG 3350, 0.2 M Sodium Acetate, 90 mM glycine, 10 mM sodium chloride, 10 mM Tris, 0.5 mM dithiothreitol, , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.8 α = 90 b = 86.326 β = 110.92 c = 83.543 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD MIRRORS 2008-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 50 90.4 0.078 10 3.7 49163 1
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) 2 2.03 71 0.367 2 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2OBR 2 35.46 48254 2597 98.2 0.191 0.189 0.2003 0.24 0.2414 RANDOM 24.17
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.481 r_dihedral_angle_4_deg 21.107 r_dihedral_angle_3_deg 15.335 r_dihedral_angle_1_deg 7.859 r_scangle_it 5.014 r_scbond_it 3.231 r_mcangle_it 2.316 r_angle_refined_deg 1.833 r_mcbond_it 1.376 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.481 r_dihedral_angle_4_deg 21.107 r_dihedral_angle_3_deg 15.335 r_dihedral_angle_1_deg 7.859 r_scangle_it 5.014 r_scbond_it 3.231 r_mcangle_it 2.316 r_angle_refined_deg 1.833 r_mcbond_it 1.376 r_chiral_restr 0.158 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4808 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling