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Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PUS PDB entry 2PUS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 10% PEG 3350, 0.4M LiNO3, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 4.08 69.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.838 α = 90 b = 122.838 β = 90 c = 354.255 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 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 3.15 36.664 98.4 0.121 0.121 5.1 6.5 27660 27660
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 3.15 3.32 98.6 0.356 0.356 1.9 4.2 3962
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 (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 2PUS 3.15 20 27545 27545 1393 97.5 0.211 0.209 0.206 0.235 0.2301 RANDOM 63.897
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] -0.34 -0.17 -0.34 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 16.509 r_dihedral_angle_1_deg 4.716 r_angle_refined_deg 0.962 r_scangle_it 0.807 r_mcangle_it 0.504 r_scbond_it 0.447 r_nbtor_refined 0.297 r_mcbond_it 0.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 16.509 r_dihedral_angle_1_deg 4.716 r_angle_refined_deg 0.962 r_scangle_it 0.807 r_mcangle_it 0.504 r_scbond_it 0.447 r_nbtor_refined 0.297 r_mcbond_it 0.279 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.065 r_symmetry_hbond_refined 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5915 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 3
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing