3LF6

Crystal structure of HIV epitope-scaffold 4E10_1XIZA_S0_001_N


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XIZComputationally-derived model of the epitope-scaffold, based on 1XIZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298DI-AMMONIUM PHOSPHATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.211α = 90
b = 81.975β = 90
c = 94.219γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107IMAGE PLATERIGAKU RAXIS IV++Rigaku Varimax HR2008-01-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
11.949.2197.50.05717.24.433005322.3
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)
1.91.9795.20.3412.64.42886

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 REPLACEMENTTHROUGHOUTComputationally-derived model of the epitope-scaffold, based on 1XIZ1.931.526499142090.630.226150.223240.27917RANDOM32.353
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]
-0.40.070.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.211
r_dihedral_angle_4_deg14.779
r_dihedral_angle_3_deg12.843
r_dihedral_angle_1_deg5.156
r_scangle_it2.345
r_scbond_it1.686
r_mcangle_it1.173
r_angle_refined_deg1.056
r_mcbond_it0.763
r_angle_other_deg0.743
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.211
r_dihedral_angle_4_deg14.779
r_dihedral_angle_3_deg12.843
r_dihedral_angle_1_deg5.156
r_scangle_it2.345
r_scbond_it1.686
r_mcangle_it1.173
r_angle_refined_deg1.056
r_mcbond_it0.763
r_angle_other_deg0.743
r_symmetry_vdw_other0.354
r_symmetry_hbond_refined0.266
r_xyhbond_nbd_refined0.218
r_nbd_other0.208
r_nbd_refined0.205
r_nbtor_refined0.186
r_mcbond_other0.179
r_nbtor_other0.087
r_chiral_restr0.061
r_symmetry_vdw_refined0.053
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2448
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms15

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling