4CYZ

Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with avian receptor analog LSTA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CYVPDB ENTRY 4CYV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
118 PERCENT PEG 2000MME AND 0.1 M BICINE PH 9.0
Crystal Properties
Matthews coefficientSolvent content
3.0159.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.07α = 90
b = 230.58β = 110.41
c = 68.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.462.8699.10.119.54750502
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)
12.42.5399.20.744

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 4CYV2.4115.2971241377099.020.207240.205290.24389RANDOM47.615
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]
1.68-0.010.69-1.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.499
r_dihedral_angle_3_deg15.989
r_dihedral_angle_4_deg13.873
r_dihedral_angle_1_deg5.489
r_angle_refined_deg1.094
r_mcangle_it0.519
r_scbond_it0.388
r_mcbond_it0.282
r_chiral_restr0.073
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.499
r_dihedral_angle_3_deg15.989
r_dihedral_angle_4_deg13.873
r_dihedral_angle_1_deg5.489
r_angle_refined_deg1.094
r_mcangle_it0.519
r_scbond_it0.388
r_mcbond_it0.282
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.004
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 Atoms11401
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms405

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing