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Structure of the C-terminal dimerization domain of infectious bronchitis virus nucleocapsid protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GE7 PDB ENTRY 2GE7 4 copies
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 298 30% PEG 4000, 100 mM Tris-HCl pH 8.6, 800 mM LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.99 α = 90 b = 128.534 β = 90 c = 71.435 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 178 CCD ADSC QUANTUM 4 Bent conical Si-mirror (Rh coated).
Bent Ge(111) monochromator 2003-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 129.473 95.8 0.115 0.115 4.8 4.4 69504 66258 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 97.3 0.013 0.01276 0.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GE7 4 copies 2.2 47.78 2 69504 51179 2615 100 0.24 0.24 0.237 0.2519 0.291 RANDOM 32.178
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] -0.02 0.08 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.144 r_dihedral_angle_3_deg 19.133 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_1_deg 8.373 r_scangle_it 4.531 r_scbond_it 2.906 r_angle_refined_deg 1.919 r_mcangle_it 1.719 r_mcbond_it 1.066 r_symmetry_hbond_refined 0.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.144 r_dihedral_angle_3_deg 19.133 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_1_deg 8.373 r_scangle_it 4.531 r_scbond_it 2.906 r_angle_refined_deg 1.919 r_mcangle_it 1.719 r_mcbond_it 1.066 r_symmetry_hbond_refined 0.473 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.142 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6881 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection CCP4 data scaling PHASER phasing CNS phasing