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Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 5% PEG 3350, 0.4M LiNO3, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 4.23 70.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.801 α = 90 b = 123.801 β = 90 c = 361.843 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 315 2007-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.975 ESRF ID29
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 2.7 107.215 95 0.1 0.1 4.9 12.2 43251 43251
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) 2.7 2.85 96.3 0.434 0.434 1.7 12.5 6265
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 (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 2.7 40 43248 43248 2195 93.93 0.223 0.221 0.2424 0.256 0.2708 RANDOM 48.396
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] 0.06 0.03 0.06 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.301 r_dihedral_angle_4_deg 20.276 r_dihedral_angle_3_deg 18.554 r_dihedral_angle_1_deg 5.559 r_scangle_it 2.103 r_angle_refined_deg 1.257 r_scbond_it 1.221 r_mcangle_it 0.997 r_mcbond_it 0.558 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.301 r_dihedral_angle_4_deg 20.276 r_dihedral_angle_3_deg 18.554 r_dihedral_angle_1_deg 5.559 r_scangle_it 2.103 r_angle_refined_deg 1.257 r_scbond_it 1.221 r_mcangle_it 0.997 r_mcbond_it 0.558 r_nbtor_refined 0.301 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.087 r_symmetry_hbond_refined 0.041 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5853 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection REFMAC phasing