5AJM

H5 (VN1194) Asn186Lys Mutant Haemagglutinin in Complex with Avian Receptor Analogue 3'SLN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BGWPDB ENTRY 4BGW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M HEPES/MOPS PH 7.0, 0.05 M MGCL2, 28-30% PEG 550 MME, SEEDED WITH CRUSHED WILD-TYPE VN1194 HA CRYSTALS.
Crystal Properties
Matthews coefficientSolvent content
3.7467

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.58α = 90
b = 101.58β = 90
c = 452.98γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
12.4550.7999.20.0813.17.8334982.7
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)
12.452.5898.10.682.77.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4BGW2.45150.9931800169799.120.201710.200380.22665RANDOM78.353
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]
1.90.951.9-6.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_3_deg14.726
r_dihedral_angle_4_deg14.659
r_dihedral_angle_1_deg5.559
r_scbond_it2.456
r_mcangle_it2.264
r_mcbond_it1.368
r_mcbond_other1.367
r_angle_refined_deg1.052
r_angle_other_deg0.672
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_3_deg14.726
r_dihedral_angle_4_deg14.659
r_dihedral_angle_1_deg5.559
r_scbond_it2.456
r_mcangle_it2.264
r_mcbond_it1.368
r_mcbond_other1.367
r_angle_refined_deg1.052
r_angle_other_deg0.672
r_chiral_restr0.057
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms3860
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing