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The 2.6A structure of Infectious Bursal Virus Derived T=1 Particles
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WCD pdb entry 1WCD
Crystallization Crystal Properties Matthews coefficient Solvent content 2.96 58.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 326.3 α = 90 b = 326.3 β = 90 c = 326.3 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MAR CCD 225 mm 2005-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
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 2.6 40 89.38 0.186 2.2 323420 323420
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 1WCD 2.6 19.97 350422 295435 15643 88.77 0.25475 0.25475 0.25409 0.2739 0.26698 0.2808 RANDOM 12.042
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 33.809 r_dihedral_angle_4_deg 20.787 r_dihedral_angle_3_deg 17.733 r_dihedral_angle_1_deg 7.273 r_scangle_it 1.598 r_angle_refined_deg 1.282 r_scbond_it 0.977 r_mcangle_it 0.535 r_nbtor_refined 0.312 r_mcbond_it 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.809 r_dihedral_angle_4_deg 20.787 r_dihedral_angle_3_deg 17.733 r_dihedral_angle_1_deg 7.273 r_scangle_it 1.598 r_angle_refined_deg 1.282 r_scbond_it 0.977 r_mcangle_it 0.535 r_nbtor_refined 0.312 r_mcbond_it 0.303 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.08 r_metal_ion_refined 0.079 r_symmetry_metal_ion_refined 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 64321 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction AMoRE phasing