5GJS

Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LZJ3LZJ, 3NFS
experimental modelPDB 3NFS3LZJ, 3NFS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES and 16% PEG 550MME
Crystal Properties
Matthews coefficientSolvent content
2.8556.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.162α = 90
b = 130.162β = 90
c = 365.853γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97914SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.95093.80.1612.96.52520146.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.931000.82.66.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3LZJ, 3NFS2.947.9823695123892.710.25360.25090.3035RANDOM51.878
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]
-0.35-0.18-0.351.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.29
r_dihedral_angle_3_deg15.583
r_dihedral_angle_4_deg13.602
r_dihedral_angle_1_deg6.029
r_mcangle_it4.991
r_scbond_it4.16
r_mcbond_it3.147
r_angle_refined_deg1.353
r_chiral_restr0.083
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.29
r_dihedral_angle_3_deg15.583
r_dihedral_angle_4_deg13.602
r_dihedral_angle_1_deg6.029
r_mcangle_it4.991
r_scbond_it4.16
r_mcbond_it3.147
r_angle_refined_deg1.353
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7028
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms42

Software

Software
Software NamePurpose
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data reduction