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Crystal structure of infectious bursal disease virus VP1 polymerase incubated with an oligopeptide mimicking the VP3 C-terminus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PUS VP1 polymease apo form structure (PDB code 2PUS)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 10-12% PEG 3350, 0.3-0.5M LiNO3, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.07 69.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.913 α = 90 b = 121.913 β = 90 c = 359.426 γ = 120
Symmetry Space Group P 61 2 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 4 2006-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 3.48 40 96.4 0.11 10.3 4.7 20344 20344
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) 3.5 3.65 99.3 0.54 2.2 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT VP1 polymease apo form structure (PDB code 2PUS) 3.48 19.98 20344 20247 1039 96.54 0.245 0.243 0.241 0.281 0.2824 RANDOM 77.518
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] -0.04 -0.02 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.575 r_dihedral_angle_3_deg 18.33 r_dihedral_angle_4_deg 15.094 r_dihedral_angle_1_deg 4.789 r_scangle_it 1.036 r_angle_refined_deg 1.023 r_mcangle_it 0.685 r_scbond_it 0.619 r_mcbond_it 0.415 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.575 r_dihedral_angle_3_deg 18.33 r_dihedral_angle_4_deg 15.094 r_dihedral_angle_1_deg 4.789 r_scangle_it 1.036 r_angle_refined_deg 1.023 r_mcangle_it 0.685 r_scbond_it 0.619 r_mcbond_it 0.415 r_nbtor_refined 0.302 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5927 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ProDC data collection AMoRE phasing