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Structure of the N-terminal domain of avian infectious bronchitis virus nucleocapsid protein (strain Gray) in a novel dimeric arrangement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BTL PDB ID 2BTL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 25 % PEG 4000,100 mM MES Sodium Salt, pH 6.2, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.055 α = 90 b = 46.21 β = 121.06 c = 74.176 γ = 90
Symmetry Space Group C 1 2 1
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 1.3 50 87.9 0.056 0.056 49.3 3.3 90638 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) 1.3 1.4 99.9 0.227 0.227 49.3 3.3
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 PDB ID 2BTL 1.3 25.42 60751 3256 89.53 0.20737 0.20534 0.2042 0.24612 0.2447 RANDOM 17.148
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] -0.13 -0.49 0.13 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.3 r_dihedral_angle_4_deg 23.045 r_dihedral_angle_3_deg 14.457 r_dihedral_angle_1_deg 7.651 r_scangle_it 7.605 r_scbond_it 6.06 r_mcangle_it 4.413 r_mcbond_it 3.358 r_sphericity_free 3.255 r_sphericity_bonded 2.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.3 r_dihedral_angle_4_deg 23.045 r_dihedral_angle_3_deg 14.457 r_dihedral_angle_1_deg 7.651 r_scangle_it 7.605 r_scbond_it 6.06 r_mcangle_it 4.413 r_mcbond_it 3.358 r_sphericity_free 3.255 r_sphericity_bonded 2.251 r_angle_refined_deg 2.23 r_rigid_bond_restr 2.196 r_symmetry_hbond_refined 0.936 r_symmetry_vdw_refined 0.689 r_nbtor_refined 0.322 r_xyhbond_nbd_refined 0.29 r_nbd_refined 0.239 r_chiral_restr 0.148 r_bond_refined_d 0.026 r_gen_planes_refined 0.016 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection CCP4 data scaling