2B1A

Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG1033 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 DROP29813.75% PEG 20000, 0.05M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9558

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.716α = 90
b = 96.89β = 90
c = 97.018γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98397SSRLBL11-1

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
12.34831.3198.60.05731.93.72498624986-356
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)
12.3482.3992.80.4882.363.11118

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 2B0S2.34831.31237322373212081000.212870.212870.211180.24446RANDOM59.833
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]
-0.520.6-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.416
r_dihedral_angle_4_deg15.236
r_dihedral_angle_3_deg14.904
r_dihedral_angle_1_deg6.726
r_scangle_it1.83
r_angle_refined_deg1.328
r_scbond_it1.222
r_angle_other_deg0.849
r_mcangle_it0.739
r_mcbond_it0.628
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.416
r_dihedral_angle_4_deg15.236
r_dihedral_angle_3_deg14.904
r_dihedral_angle_1_deg6.726
r_scangle_it1.83
r_angle_refined_deg1.328
r_scbond_it1.222
r_angle_other_deg0.849
r_mcangle_it0.739
r_mcbond_it0.628
r_symmetry_vdw_other0.246
r_nbd_refined0.199
r_nbd_other0.197
r_symmetry_vdw_refined0.185
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.13
r_xyhbond_nbd_other0.11
r_mcbond_other0.099
r_nbtor_other0.085
r_chiral_restr0.079
r_symmetry_hbond_refined0.074
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3440
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction