7B4W

Broadly neutralizing DARPin bnD.3 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-IF (BG505)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION277.150.2M Ca Acetate, 0.1 Na Acetate pH 5.5, 30% PEG 2K MME
Crystal Properties
Matthews coefficientSolvent content
2.0840.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.4α = 90
b = 67.06β = 90
c = 93.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00004SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.954.4299.60.1050.1210.9968.093.9444791032.086
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.950.682

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 REPLACEMENTTHROUGHOUTin house model1.946.624254127999.910.183160.180770.22732RANDOM31.731
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]
2.22-0.48-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.694
r_dihedral_angle_3_deg15.582
r_dihedral_angle_4_deg6.514
r_long_range_B_refined6.433
r_long_range_B_other6.432
r_dihedral_angle_1_deg6.138
r_scangle_other2.371
r_angle_refined_deg1.787
r_mcangle_it1.606
r_mcangle_other1.606
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.694
r_dihedral_angle_3_deg15.582
r_dihedral_angle_4_deg6.514
r_long_range_B_refined6.433
r_long_range_B_other6.432
r_dihedral_angle_1_deg6.138
r_scangle_other2.371
r_angle_refined_deg1.787
r_mcangle_it1.606
r_mcangle_other1.606
r_scbond_it1.495
r_scbond_other1.495
r_angle_other_deg1.489
r_mcbond_other1.047
r_mcbond_it1.046
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2622
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction