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Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LZJ 3LZJ, 3NFS experimental model PDB 3NFS 3LZJ, 3NFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M MES and 16% PEG 550MME
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.162 α = 90 b = 130.162 β = 90 c = 365.853 γ = 120
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 315r 2014-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97914 SSRF BL17U
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 2.9 50 93.8 0.16 12.9 6.5 25201 46.6
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 2.9 3 100 0.8 2.6 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LZJ, 3NFS 2.9 47.98 23695 1238 92.71 0.2536 0.2509 0.3035 0.2224 RANDOM 51.878
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] -0.35 -0.18 -0.35 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.29 r_dihedral_angle_3_deg 15.583 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_1_deg 6.029 r_mcangle_it 4.991 r_scbond_it 4.16 r_mcbond_it 3.147 r_angle_refined_deg 1.353 r_chiral_restr 0.083 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.29 r_dihedral_angle_3_deg 15.583 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_1_deg 6.029 r_mcangle_it 4.991 r_scbond_it 4.16 r_mcbond_it 3.147 r_angle_refined_deg 1.353 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7028 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data scaling PHENIX phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction HKL-2000 data reduction