2XA3

crystal structure of the broadly neutralizing llama VHH D7 and its mode of HIV-1 gp120 interaction


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCVPDB ENTRY 1HCV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
165 MG/ML OF D7 PROTEIN IN A SOLUTION OF 20MM HEPES PH 7, 0.1 M NACL MIXED WITH AN EQUAL VOLUME OF 100MM SODIUM CACODYLATE PH 6, 20 MM MAGNESIUM ACETATE, 1.7M AMMONIUM SULFATE AND 19 % GLYCEROL WELL CONDITION
Crystal Properties
Matthews coefficientSolvent content
2.8757.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.37α = 90
b = 62.18β = 90
c = 62.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100MARRESEARCHMIRRORS2009-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.54494.10.052332269513.39
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)
11.568.70.26.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1HCV1.524.0270.0822364113592.930.1670.16570.1935
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]
-1.2255-0.41921.6447
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.816
f_angle_d1.065
f_chiral_restr0.071
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms977
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms20

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing