3NTC

Crystal structure of KD-247 Fab, an anti-V3 antibody that inhibits HIV-1 Entry


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T3FPDB entry 1T3F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.9294Ammonium Sulfate, Sodium Acetate, pH 3.9, vapor diffusion, sitting drop, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4950.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.06α = 90
b = 69.18β = 90
c = 111.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDNOIR-1MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0ALS4.2.2

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
11.5519.7588.40.071115.5668504
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)
1.551.6187.10.4852.45.025995

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 1T3F1.5519.751.3368478274898.670.18360.18190.2218
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]
-1.4325.2789-3.8468
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.573
f_angle_d1.156
f_chiral_restr0.067
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3342
Nucleic Acid Atoms
Solvent Atoms501
Heterogen Atoms62

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction