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Crystal structure of in cellulo Wild Type Cypovirus Polyhedra
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 300 In vivo crystallization
Crystal Properties Matthews coefficient Solvent content 1.62 24.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.42 α = 90 b = 103.42 β = 90 c = 103.42 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 CCD RAYONIX MX325HE 2016-04-25 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) 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 1.68 50 99.4 6.06 7.8 20993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.78
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 THROUGHOUT 2OH6 1.68 42.22 18910 2083 99.44 0.15221 0.14759 0.1475 0.1955 0.1954 RANDOM 12.501
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 37.835 r_dihedral_angle_4_deg 23.308 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_1_deg 6.851 r_long_range_B_refined 3.78 r_angle_refined_deg 1.951 r_scbond_it 1.819 r_mcangle_it 1.203 r_mcbond_it 0.799 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.835 r_dihedral_angle_4_deg 23.308 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_1_deg 6.851 r_long_range_B_refined 3.78 r_angle_refined_deg 1.951 r_scbond_it 1.819 r_mcangle_it 1.203 r_mcbond_it 0.799 r_chiral_restr 0.14 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2009 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement