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Crystal structure of P[6] rotavirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M HEPES sodium pH 7.5, 1.5 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.691 α = 90 b = 76 β = 91.89 c = 73.881 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 RAYONIX MX-225 2018-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.55 73.84 95.8 0.042 0.05 0.027 0.999 13.3 3.4 87191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 95.4 0.476 0.565 0.3 0.905 3.4
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 5vx8 1.55 73.84 82770 4399 95.43 0.2004 0.1986 0.2083 0.2325 0.2395 RANDOM 23.08
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] -2.23 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.879 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_1_deg 8.521 r_angle_refined_deg 1.546 r_angle_other_deg 1.382 r_chiral_restr 0.082 r_gen_planes_refined 0.017 r_bond_refined_d 0.014 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.879 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_1_deg 8.521 r_angle_refined_deg 1.546 r_angle_other_deg 1.382 r_chiral_restr 0.082 r_gen_planes_refined 0.017 r_bond_refined_d 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5186 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 14
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing