3LG7

Crystal structure of HIV epitope-scaffold 4E10_S0_1EZ3A_002_C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EZ3Computationally-derived model of the epitope-scaffold, based on 1EZ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277Ammonium sulfate, bis Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.7874.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.6α = 90
b = 94.87β = 90
c = 108.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107CCDRIGAKU SATURN 944+Rigaku Varimax HF2008-05-09MSINGLE 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
12.528.8299.50.1076.64.53332203322066.7
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)
2.52.5996.80.42923.783180

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 1EZ32.528.823312333123167299.390.259230.257020.30121RANDOM38.599
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]
0.06-0.04-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.867
r_dihedral_angle_4_deg21.723
r_dihedral_angle_3_deg17.272
r_scangle_it4.297
r_dihedral_angle_1_deg3.952
r_scbond_it2.96
r_mcbond_it1.683
r_mcangle_it1.667
r_angle_refined_deg1.189
r_angle_other_deg0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.867
r_dihedral_angle_4_deg21.723
r_dihedral_angle_3_deg17.272
r_scangle_it4.297
r_dihedral_angle_1_deg3.952
r_scbond_it2.96
r_mcbond_it1.683
r_mcangle_it1.667
r_angle_refined_deg1.189
r_angle_other_deg0.73
r_symmetry_vdw_other0.357
r_nbd_refined0.246
r_mcbond_other0.222
r_symmetry_hbond_refined0.199
r_nbtor_refined0.198
r_nbd_other0.194
r_xyhbond_nbd_refined0.186
r_symmetry_vdw_refined0.153
r_nbtor_other0.089
r_chiral_restr0.062
r_bond_refined_d0.014
r_bond_other_d0.005
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 Atoms3096
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms55

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling