☰ Navigation Tabs
Native Tipula oleracea Nudivirus polyhedrin - 1960
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 293 Protein natively forms crystals inside insect cells.
Crystal Properties Matthews coefficient Solvent content 1.59 22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.389 α = 90 b = 53.389 β = 90 c = 105.578 γ = 120
Symmetry Space Group P 32 2 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 EIGER2 S 9M 2021-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXm 0.63282 Diamond VMXm
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.69 28 94.02 0.793 0.967 9.91 19.6 19056 16.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.75 0.321
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8BC5 1.69 28 1.34 18969 1901 94.06 0.1911 0.189 0.1886 0.2095 0.2075 18.32
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 13.2711 f_angle_d 0.5676 f_chiral_restr 0.0365 f_plane_restr 0.0032 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1833 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Coot model building xia2.multiplex data reduction DIALS data reduction xia2.multiplex data scaling DIALS data scaling CRANK phasing