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Crystal structure of 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 24.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.328 α = 90 b = 103.328 β = 90 c = 103.328 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 2011-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.68880 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 1.78 50 100 7.8 4.7 17724
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 1.78 1.81
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OH6 1.78 32.68 16710 898 99.55 0.16558 0.16365 0.20118 0.1686 RANDOM 6.934
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 37.626 r_dihedral_angle_4_deg 23.387 r_dihedral_angle_3_deg 11.951 r_dihedral_angle_1_deg 6.516 r_long_range_B_refined 2.766 r_angle_refined_deg 1.604 r_scbond_it 0.928 r_mcangle_it 0.654 r_mcbond_it 0.379 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.626 r_dihedral_angle_4_deg 23.387 r_dihedral_angle_3_deg 11.951 r_dihedral_angle_1_deg 6.516 r_long_range_B_refined 2.766 r_angle_refined_deg 1.604 r_scbond_it 0.928 r_mcangle_it 0.654 r_mcbond_it 0.379 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 132 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling