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Crystal structure of Cypovirus Polyhedra mutant fused with CLN025
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 IN CELL 293 in cell crystallization
Crystal Properties Matthews coefficient Solvent content 1.65 25.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.52 α = 90 b = 104.52 β = 90 c = 104.52 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 2019-12-05 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 1.75 50 100 0.98 5.84 211.2 19331
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 1.75 1.76 0.319
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2OH6 1.75 42.707 19331 1923 99.99 0.176 0.173 0.1675 0.2091 0.2047 9.137
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 r_dihedral_angle_2_deg 34.174 r_dihedral_angle_4_deg 19.485 r_dihedral_angle_3_deg 11.991 r_dihedral_angle_1_deg 7.259 r_lrange_it 2.669 r_lrange_other 2.624 r_scangle_it 1.797 r_scangle_other 1.796 r_angle_refined_deg 1.544 r_angle_other_deg 1.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.174 r_dihedral_angle_4_deg 19.485 r_dihedral_angle_3_deg 11.991 r_dihedral_angle_1_deg 7.259 r_lrange_it 2.669 r_lrange_other 2.624 r_scangle_it 1.797 r_scangle_other 1.796 r_angle_refined_deg 1.544 r_angle_other_deg 1.372 r_mcangle_it 1.269 r_mcangle_other 1.269 r_scbond_it 1.137 r_scbond_other 1.137 r_mcbond_it 0.773 r_mcbond_other 0.771 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.198 r_nbd_other 0.196 r_nbtor_refined 0.169 r_symmetry_nbd_other 0.165 r_symmetry_xyhbond_nbd_refined 0.138 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2046 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XSCALE data scaling MOLREP phasing Coot model building XDS data reduction