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Structure of Finch Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 Magnesium chloride, TRIS, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.496 α = 107.09 b = 172.063 β = 97.93 c = 245.616 γ = 93.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2M-F 2018-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99986 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 49.95 94.7 0.271 0.976 4.64 2.7 377799 38.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.81 96.4 1.13 0.52 1.12 2.77
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 FREE R-VALUE 4FMG 2.65 49.94 377799 3778 94.7 0.2448 0.2446 0.2457 0.2667 0.2678 RANDOM 33.597
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] 6.62 0.27 0.25 -1.72 -1.64 -3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.036 r_dihedral_angle_4_deg 17.889 r_dihedral_angle_3_deg 14.101 r_dihedral_angle_1_deg 7.142 r_angle_other_deg 2.405 r_angle_refined_deg 1.343 r_chiral_restr 0.053 r_bond_other_d 0.037 r_gen_planes_other 0.008 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.036 r_dihedral_angle_4_deg 17.889 r_dihedral_angle_3_deg 14.101 r_dihedral_angle_1_deg 7.142 r_angle_other_deg 2.405 r_angle_refined_deg 1.343 r_chiral_restr 0.053 r_bond_other_d 0.037 r_gen_planes_other 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 78546 Nucleic Acid Atoms Solvent Atoms 2378 Heterogen Atoms 663
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction