3UJI

Crystal structure of anti-HIV-1 V3 Fab 2558 in complex with MN peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.529685mM Hepes-Na, 15% Glycerol, 17% PEG 4k, 8.5% Isopropanol, pH 7.5, EVAPORATION, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.8857.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.351α = 90
b = 73.097β = 121.98
c = 88.662γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.97854NSLSX4C

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
11.65099.20.05429.16.1731907260811
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)
11.61.6398.40.431

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.65072546688843662990.16260.160950.19378RANDOM21.42
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]
0.21-0.28-0.32-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.998
r_dihedral_angle_4_deg14.034
r_dihedral_angle_3_deg11.898
r_dihedral_angle_1_deg7.251
r_angle_refined_deg2.633
r_chiral_restr0.215
r_bond_refined_d0.028
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.998
r_dihedral_angle_4_deg14.034
r_dihedral_angle_3_deg11.898
r_dihedral_angle_1_deg7.251
r_angle_refined_deg2.633
r_chiral_restr0.215
r_bond_refined_d0.028
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3358
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms39

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling