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crystal structure of avian influenza virus PA_N in complex with AMP
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, SITTING DROP 6.5 291 17.5% PEG3350(w/v), 100mM MgAc, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.617 α = 96.02 b = 60.029 β = 96.22 c = 67.177 γ = 109.35
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 2009-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1 Photon Factory BL-17A
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 1.8 50 96 0.054 63099 65112
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) 1.8 1.9 96 0.128 7817
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 1.81 50 59908 3187 91.76 0.20908 0.20622 0.2013 0.2627 0.2534 RANDOM 29.176
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] 2.27 2.07 1.1 0.08 0.55 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_4_deg 24.279 r_dihedral_angle_3_deg 19.128 r_dihedral_angle_1_deg 6.689 r_scangle_it 6.46 r_scbond_it 4.051 r_mcangle_it 2.536 r_angle_refined_deg 2.186 r_mcbond_it 1.452 r_chiral_restr 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.459 r_dihedral_angle_4_deg 24.279 r_dihedral_angle_3_deg 19.128 r_dihedral_angle_1_deg 6.689 r_scangle_it 6.46 r_scbond_it 4.051 r_mcangle_it 2.536 r_angle_refined_deg 2.186 r_mcbond_it 1.452 r_chiral_restr 0.189 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5864 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 27
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling