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Influenza virus (VN1194) H5 HA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JSM PDB ENTRY 1JSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 15/4 EO/OH, Ammonium sulfate, Bis-tris, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.84 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.678 α = 90 b = 100.563 β = 111.39 c = 160.13 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 IMAGE PLATE RIGAKU RAXIS IV 2006-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.8 30 76.9 0.097 8.7 2.7 48951
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 2.8 2.93 80.2 0.496 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1JSM 2.8 30 48951 48951 2498 76.8 0.244 0.241 0.2336 0.302 0.2891 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.461 r_dihedral_angle_3_deg 20.65 r_dihedral_angle_4_deg 20.319 r_dihedral_angle_1_deg 7.598 r_scangle_it 2.837 r_scbond_it 1.669 r_angle_refined_deg 1.665 r_mcangle_it 1.269 r_mcbond_it 0.698 r_symmetry_hbond_refined 0.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.461 r_dihedral_angle_3_deg 20.65 r_dihedral_angle_4_deg 20.319 r_dihedral_angle_1_deg 7.598 r_scangle_it 2.837 r_scbond_it 1.669 r_angle_refined_deg 1.665 r_mcangle_it 1.269 r_mcbond_it 0.698 r_symmetry_hbond_refined 0.516 r_nbtor_refined 0.321 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.238 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_refined 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 11514 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing