3QHF

Crystal Structure of Fab del2D1, a deletion variant of anti-influenza antibody 2D1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QHZ3QHZ (chains H and L)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27320% PEG 4000, 100 mM sodium acetate, and 200 mM magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.4950.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.913α = 90
b = 69.68β = 90
c = 97.678γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARMOSAIC 300 mm CCD2010-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.655099.7558665573011
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7199.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3QHZ (chains H and L)1.655505586655730283098.10.18450.18450.18310.2092Random
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]
-4.86874.81740.0513
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.26
f_angle_d1.227
f_chiral_restr0.078
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3290
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms

Software

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