3LEF

Crystal structure of HIV epitope-scaffold 4E10_S0_1Z6NA_001


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z6NComputationally-derived model of the epitope-scaffold, based on 1Z6N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277Na/K tartrate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.8568.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.41α = 90
b = 56.41β = 90
c = 324.13γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107IMAGE PLATERIGAKU RAXIS IV++Rigaku Varimax HR2007-04-17MSINGLE 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
12.348.393.70.08698.4137701377056.3
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)
2.32.3891.50.3733.96.831304

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 1Z6N2.346.781306466793.470.259780.258310.29042RANDOM49.573
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]
-0.22-0.11-0.220.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.951
r_dihedral_angle_4_deg19.905
r_dihedral_angle_3_deg16.259
r_dihedral_angle_1_deg4.95
r_scangle_it2.547
r_scbond_it1.662
r_angle_refined_deg1.146
r_mcangle_it1.035
r_angle_other_deg0.781
r_mcbond_it0.666
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.951
r_dihedral_angle_4_deg19.905
r_dihedral_angle_3_deg16.259
r_dihedral_angle_1_deg4.95
r_scangle_it2.547
r_scbond_it1.662
r_angle_refined_deg1.146
r_mcangle_it1.035
r_angle_other_deg0.781
r_mcbond_it0.666
r_symmetry_vdw_other0.214
r_nbd_refined0.203
r_nbd_other0.203
r_xyhbond_nbd_refined0.195
r_nbtor_refined0.18
r_symmetry_hbond_refined0.178
r_mcbond_other0.133
r_symmetry_vdw_refined0.098
r_nbtor_other0.091
r_chiral_restr0.07
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 Atoms1261
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms4

Software

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