5GJT

Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 3E1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GJS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M Na HEPES, 20% PEG400 and 0.1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.8957.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.806α = 90
b = 130.806β = 90
c = 366.938γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSDECTRIS PILATUS3 S 6M2015-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U11.0000SSRFBL19U1

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
13.1501000.1116.712.62241762.9
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)
13.13.211000.473.913.1

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 REPLACEMENTTHROUGHOUT5GJS3.15021207114399.60.2180.2160.259RANDOM70.49
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]
0.850.420.85-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.453
r_dihedral_angle_3_deg14.924
r_dihedral_angle_4_deg11.556
r_mcangle_it4.47
r_dihedral_angle_1_deg4.467
r_scbond_it3.309
r_mcbond_it2.778
r_angle_refined_deg1.283
r_chiral_restr0.067
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.453
r_dihedral_angle_3_deg14.924
r_dihedral_angle_4_deg11.556
r_mcangle_it4.47
r_dihedral_angle_1_deg4.467
r_scbond_it3.309
r_mcbond_it2.778
r_angle_refined_deg1.283
r_chiral_restr0.067
r_bond_refined_d0.011
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7069
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-3000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction