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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 3KC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG 3350, 200MM NACL, 100MM TRIS PH 8.5, PROTEIN CONCENTRATION 24.4 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 1.92 35.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.042 α = 90 b = 57.007 β = 102.4 c = 83.081 γ = 90
Symmetry Space Group P 1 21 1
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 SATURN 944++ MIRRORS 2009-11-09 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 2.3 81.14 98.1 0.029 54 3.5 16536
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 2.3 2.34 82 0.046 2.2
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 3KC6 2.3 50 16526 840 0.18 0.176 0.1801 0.237 0.1806 RANDOM 12.98
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] 0.33 -0.46 -0.26 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.474 r_dihedral_angle_4_deg 20.268 r_dihedral_angle_3_deg 14.815 r_dihedral_angle_1_deg 6.109 r_scangle_it 3.142 r_scbond_it 1.966 r_angle_refined_deg 1.377 r_mcangle_it 1.373 r_angle_other_deg 0.892 r_mcbond_it 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.474 r_dihedral_angle_4_deg 20.268 r_dihedral_angle_3_deg 14.815 r_dihedral_angle_1_deg 6.109 r_scangle_it 3.142 r_scbond_it 1.966 r_angle_refined_deg 1.377 r_mcangle_it 1.373 r_angle_other_deg 0.892 r_mcbond_it 0.73 r_mcbond_other 0.138 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 3100 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling