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Apex domain deletion mutant of bacteriophage P2 central spike protein, membrane-piercing module
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 26-33% Pentaerythritol ethoxylate (15/4 EO/OH) aka PEE-797, 100 mM Bis-Tris or MES pH 6.0-6.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.52 α = 91.61 b = 49.91 β = 88.25 c = 72.93 γ = 111.65
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 EIGER X 9M 2020-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.774900 APS 21-ID-D
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 0.9 26.73 94.5 0.083 0.995 9.69 3.33 821847 7.29
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 0.9 0.93 85.9 0.544 0.861 2.07 3.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 0.9 26.73 1.06 821287 8211 94.42 0.1164 0.1163 0.1165 0.127 0.1269 13.6
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 f_dihedral_angle_d 8.6824 f_angle_d 1.0783 f_chiral_restr 0.0942 f_plane_restr 0.0209 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4446 Nucleic Acid Atoms Solvent Atoms 1176 Heterogen Atoms 50
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building PHENIX refinement