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Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 5% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.084 α = 90 b = 65.696 β = 90 c = 96.855 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944+ MIRRORS 2009-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 2.05 50 98.7 0.079 9.1 5.6 13728
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) 1 2.05 2.09 88.5 0.328 4
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 3CW4 2.05 50 13682 684 0.204 0.202 0.2174 0.245 0.2689 RANDOM 9.38
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] 0.29 -1.01 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.82 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_1_deg 5.77 r_scangle_it 2.396 r_scbond_it 1.453 r_angle_refined_deg 1.187 r_mcangle_it 1.054 r_angle_other_deg 0.834 r_mcbond_it 0.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.82 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_1_deg 5.77 r_scangle_it 2.396 r_scbond_it 1.453 r_angle_refined_deg 1.187 r_mcangle_it 1.054 r_angle_other_deg 0.834 r_mcbond_it 0.582 r_mcbond_other 0.106 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1503 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 12
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling