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Structural insights into the multifunctional protein VP3 of Birnaviruses
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 2.5M NaCl 0.1M Sodium Acetate pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.316 α = 90 b = 68.316 β = 90 c = 71.295 γ = 90
Symmetry Space Group P 41 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 100 CCD ADSC QUANTUM 315 2006-03-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0397, 1.04, 1.037 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 20 92.7 0.077 11.8 6.2 7401 7401
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 63.5 0.305 3.4 480
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.3 20 7401 7374 344 92.58 0.226 0.224 0.222 0.264 0.2608 RANDOM 41.016
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] 0.65 0.65 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.042 r_dihedral_angle_4_deg 21.806 r_dihedral_angle_3_deg 17.694 r_dihedral_angle_1_deg 5.55 r_scangle_it 2.338 r_scbond_it 1.393 r_angle_refined_deg 1.135 r_mcangle_it 1.063 r_mcbond_it 0.607 r_nbtor_refined 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.042 r_dihedral_angle_4_deg 21.806 r_dihedral_angle_3_deg 17.694 r_dihedral_angle_1_deg 5.55 r_scangle_it 2.338 r_scbond_it 1.393 r_angle_refined_deg 1.135 r_mcangle_it 1.063 r_mcbond_it 0.607 r_nbtor_refined 0.289 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1029 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection