3LHP

Crystal structure of HIV epitope-scaffold 4E10_D0_1ISEA_004_N 4E10 Fv complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.1442.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.977α = 90
b = 88.623β = 90
c = 149.997γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray107CCDRIGAKU SATURN 944+Rigaku Varimax HF2008-03-10MSINGLE 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
12.729.5496.20.1027.13.45193561935669.7
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)
2.72.885.50.4052.22.861705

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 Fv complex, with the Fv based on PDB ID 1TZG.2.728.99192841928498096.020.247320.242670.33503RANDOM41.289
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]
-0.09-0.160.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.397
r_dihedral_angle_3_deg18.403
r_dihedral_angle_4_deg14.274
r_dihedral_angle_1_deg5.924
r_scangle_it1.435
r_angle_refined_deg1.132
r_scbond_it0.956
r_angle_other_deg0.806
r_mcangle_it0.747
r_mcbond_it0.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.397
r_dihedral_angle_3_deg18.403
r_dihedral_angle_4_deg14.274
r_dihedral_angle_1_deg5.924
r_scangle_it1.435
r_angle_refined_deg1.132
r_scbond_it0.956
r_angle_other_deg0.806
r_mcangle_it0.747
r_mcbond_it0.541
r_nbd_refined0.213
r_nbd_other0.195
r_symmetry_vdw_other0.192
r_symmetry_vdw_refined0.187
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.104
r_nbtor_other0.084
r_chiral_restr0.051
r_mcbond_other0.05
r_bond_refined_d0.009
r_bond_other_d0.007
r_xyhbond_nbd_other0.004
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_symmetry_hbond_other
r_metal_ion_other
r_metal_ion_refined
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5112
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms4

Software

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