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The crystal structure of avian influenza virus PA_N in complex with UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 17.5% PEG3350(w/v), 100mM MgAc, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.555854 20.943727
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.132 α = 96.28 b = 59.695 β = 96.65 c = 66.85 γ = 109.44
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 270 2009-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 50 99 0.062 54981
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) 1.9 2 95 0.251 7356
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 3EBJ 1.9 50 52165 2806 95.87 0.22056 0.21757 0.2173 0.27593 0.2753 RANDOM 28.867
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] 1.61 2.13 1.35 1.84 0.83 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.887 r_dihedral_angle_4_deg 22.248 r_dihedral_angle_3_deg 18.928 r_dihedral_angle_1_deg 6.045 r_scangle_it 4.413 r_scbond_it 2.878 r_mcangle_it 1.883 r_angle_refined_deg 1.639 r_mcbond_it 1.166 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.887 r_dihedral_angle_4_deg 22.248 r_dihedral_angle_3_deg 18.928 r_dihedral_angle_1_deg 6.045 r_scangle_it 4.413 r_scbond_it 2.878 r_mcangle_it 1.883 r_angle_refined_deg 1.639 r_mcbond_it 1.166 r_nbtor_refined 0.307 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.131 r_metal_ion_refined 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5874 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 25
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling