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Crystal structure of P[6] rotavirus vp8* complexed with LNFPI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate, 1.0 M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.69 α = 90 b = 75.87 β = 91.86 c = 74.927 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 PIXEL DECTRIS PILATUS3 S 6M 2019-03-01 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 1.9 74.89 97.3 0.073 0.087 0.046 0.998 12.4 3.4 48808
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 1.9 2 96.4 0.363 0.438 0.24 0.867 3.2
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 6NIW 1.9 45.95 46445 2342 97.11 0.1972 0.1947 0.2026 0.2498 0.2535 RANDOM 19.793
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] -1.27 0.95 -0.67 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_3_deg 13.104 r_dihedral_angle_4_deg 12.195 r_dihedral_angle_1_deg 8.748 r_angle_refined_deg 1.563 r_angle_other_deg 1.329 r_chiral_restr 0.075 r_gen_planes_refined 0.016 r_bond_refined_d 0.014 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_3_deg 13.104 r_dihedral_angle_4_deg 12.195 r_dihedral_angle_1_deg 8.748 r_angle_refined_deg 1.563 r_angle_other_deg 1.329 r_chiral_restr 0.075 r_gen_planes_refined 0.016 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 5188 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 58
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing