3GBM

Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ADQ1ADQ 2FK0
experimental modelPDB 2FK01ADQ 2FK0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629512% PEG 6000, 10mM sodium acetate pH 6.0 Cryoprotectant: 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.2962.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 202.761α = 90
b = 202.761β = 90
c = 202.761γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray75CCDMARMOSAIC 300 mm CCD2008-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0333APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.7491000.1318.421.476118281.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7699.90.792.0312.2

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 REPLACEMENTTHROUGHOUT1ADQ 2FK02.74967938364594.050.205860.202910.26067RANDOM41.605
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.296
r_dihedral_angle_3_deg17.182
r_dihedral_angle_4_deg16.838
r_dihedral_angle_1_deg6.964
r_scangle_it2.465
r_scbond_it1.441
r_angle_refined_deg1.432
r_mcangle_it0.899
r_angle_other_deg0.886
r_mcbond_it0.473
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.296
r_dihedral_angle_3_deg17.182
r_dihedral_angle_4_deg16.838
r_dihedral_angle_1_deg6.964
r_scangle_it2.465
r_scbond_it1.441
r_angle_refined_deg1.432
r_mcangle_it0.899
r_angle_other_deg0.886
r_mcbond_it0.473
r_chiral_restr0.08
r_mcbond_other0.079
r_bond_refined_d0.012
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13853
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms162

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling