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Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B7M PDB ENTRY 4B7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.09 M malonic acid, 0.013 M ammonium citrate tribasic, 0.006 M succinic acid, 0.015 M DL-malic acid, 0.02 M sodium acetate, 0.025 M sodium formate, 0.008 M ammonium tartrate dibasic, 0.1 M HEPES/NaOH, 10% w/v PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.93 57.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.29 α = 90 b = 202.951 β = 90 c = 143.968 γ = 90
Symmetry Space Group C 2 2 2
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 MARMOSAIC 300 mm CCD 2012-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 47.853 99.1 52272 48574 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 99.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4B7M 2.8 47.85 2 48633 46115 2458 92.9 0.19 0.18318 0.18103 0.188 0.22379 0.2269 RANDOM 48.269
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] -0.1 0.12 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.61 r_dihedral_angle_3_deg 17.025 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_1_deg 7.34 r_long_range_B_refined 6.407 r_long_range_B_other 6.404 r_scangle_other 4.429 r_mcangle_it 3.958 r_mcangle_other 3.958 r_scbond_it 2.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.61 r_dihedral_angle_3_deg 17.025 r_dihedral_angle_4_deg 16.354 r_dihedral_angle_1_deg 7.34 r_long_range_B_refined 6.407 r_long_range_B_other 6.404 r_scangle_other 4.429 r_mcangle_it 3.958 r_mcangle_other 3.958 r_scbond_it 2.798 r_scbond_other 2.798 r_mcbond_it 2.469 r_mcbond_other 2.469 r_angle_refined_deg 1.612 r_angle_other_deg 0.957 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12635 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 116
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling