2B1H

Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG29 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B0SPDB ENTRY 2B0S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29825% MPEG 5000, 0.2M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.899α = 90
b = 94.501β = 90
c = 96.617γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.00ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1267.4299.90.06919.74.83960939609-333.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.031000.6122.64.81963

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2B0S267.423757637576198299.780.206460.206460.204730.23837RANDOM35.055
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]
-1.192.5-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.917
r_dihedral_angle_3_deg15.336
r_dihedral_angle_4_deg12.231
r_dihedral_angle_1_deg7.348
r_scangle_it3.235
r_scbond_it2.38
r_angle_refined_deg1.728
r_mcangle_it1.495
r_mcbond_it1.215
r_angle_other_deg0.967
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.917
r_dihedral_angle_3_deg15.336
r_dihedral_angle_4_deg12.231
r_dihedral_angle_1_deg7.348
r_scangle_it3.235
r_scbond_it2.38
r_angle_refined_deg1.728
r_mcangle_it1.495
r_mcbond_it1.215
r_angle_other_deg0.967
r_mcbond_other0.27
r_symmetry_vdw_other0.233
r_nbd_refined0.218
r_nbd_other0.198
r_symmetry_vdw_refined0.186
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.163
r_chiral_restr0.117
r_symmetry_hbond_refined0.099
r_nbtor_other0.088
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.004
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 Atoms3449
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction