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Crystal Structure of Cypovirus Polyhedra R13A Mutant
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 7 300 IN VIVO CRYSTALLIZATION IN THE CYTOPLASM OF THE CELL, PH 7.0, TEMPERATURE 300K
Crystal Properties Matthews coefficient Solvent content 1.62 24.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.229 α = 90 b = 103.229 β = 90 c = 103.229 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 MX225HE 2011-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.6 40 100 0.132 14.2 5 24339 9.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.6 2.5 4.9
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 1.6 32.64 23019 1237 100 0.162 0.16 0.1591 0.189 0.1879 RANDOM 9.52
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 36.43 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_3_deg 11.471 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.356 r_chiral_restr 0.093 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.43 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_3_deg 11.471 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.356 r_chiral_restr 0.093 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 2003 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 73
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement