3LF9

Crystal structure of HIV epitope-scaffold 4E10_D0_1IS1A_001_C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IS1Computationally-derived model of the epitope-scaffold, based on 1IS1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277PEG 4000, Ca chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2344.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.66α = 90
b = 75.36β = 90
c = 79.61γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107CCDRIGAKU SATURN 944+Rigaku Varimax HF2008-06-04MSINGLE 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
1232.6498.30.05218.64.538462846227.7
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)
22.0789.90.18542.66755

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1IS1227.378032803239698.170.206970.204440.25969RANDOM30.398
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]
-0.05-0.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg18.106
r_dihedral_angle_3_deg13.319
r_dihedral_angle_1_deg4.013
r_scangle_it3.3
r_scbond_it2.233
r_mcangle_it1.403
r_angle_refined_deg1.004
r_mcbond_it0.938
r_angle_other_deg0.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg18.106
r_dihedral_angle_3_deg13.319
r_dihedral_angle_1_deg4.013
r_scangle_it3.3
r_scbond_it2.233
r_mcangle_it1.403
r_angle_refined_deg1.004
r_mcbond_it0.938
r_angle_other_deg0.841
r_symmetry_vdw_other0.322
r_symmetry_vdw_refined0.221
r_nbd_refined0.219
r_mcbond_other0.214
r_xyhbond_nbd_refined0.207
r_nbd_other0.202
r_symmetry_hbond_refined0.191
r_nbtor_refined0.178
r_nbtor_other0.087
r_chiral_restr0.057
r_bond_refined_d0.011
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms907
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms

Software

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