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The 627-domain from influenza A virus polymerase PB2 subunit with Glu- 627
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VY7 627-DOMAIN WITH K627 FROM PDB ENTRY 2VY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1 MICROLITRE OF 2.4 MG/ML PROTEIN SOLUTION IN 10 MM TRIS-HCL PH 7.0 AND 200 MM NACL WITH 1 MICROLITRE OF 100 MM CITRIC ACID PH 4.0-7.0 AND 1.4-1.6 M AMMONIUM SULFATE SOLUTION
Crystal Properties Matthews coefficient Solvent content 1.8 33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.5 α = 90 b = 45.7 β = 106.24 c = 60.84 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH 2007-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.15 30 92.9 0.1 5.07 2.84 42201
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 1.15 1.2 85.9 0.33 2.5 1.39
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 627-DOMAIN WITH K627 FROM PDB ENTRY 2VY7 1.2 29.21 35705 1874 93.9 0.191 0.189 0.1945 0.214 0.2152 RANDOM 9.91
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] -0.23 0.39 0.19 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.346 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_3_deg 11.929 r_dihedral_angle_1_deg 5.759 r_scangle_it 4.49 r_scbond_it 3.251 r_mcangle_it 2.298 r_mcbond_it 1.708 r_angle_refined_deg 1.537 r_angle_other_deg 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.346 r_dihedral_angle_4_deg 17.203 r_dihedral_angle_3_deg 11.929 r_dihedral_angle_1_deg 5.759 r_scangle_it 4.49 r_scbond_it 3.251 r_mcangle_it 2.298 r_mcbond_it 1.708 r_angle_refined_deg 1.537 r_angle_other_deg 1.022 r_symmetry_vdw_refined 0.322 r_symmetry_vdw_other 0.318 r_nbd_refined 0.235 r_symmetry_hbond_refined 0.215 r_nbd_other 0.179 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.085 r_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing