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Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 293 cell-free crystallization
Crystal Properties Matthews coefficient Solvent content 1.78 30.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.53 α = 90 b = 106.53 β = 90 c = 106.53 γ = 90
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 6M 2022-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.04 50 99.9 0.999 19.4 58 12981 33.27
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 2.04 2.11 0.658
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 2.04 43.49 1.34 12980 1298 99.92 0.226 0.2216 0.2231 0.2652 0.2648 34.84
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 5.7298 f_angle_d 0.9178 f_chiral_restr 0.0571 f_bond_d 0.0082 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1394 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling MOLREP phasing Coot model building XDS data reduction