2BGN

HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W1IPDB ENTRY 1W1I

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.1460.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.945α = 90
b = 170.273β = 100.93
c = 239.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
13.1530890.119.72.5977822.6
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)
13.153.26810.412.62.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1W1I3.153094691192589.60.2270.2270.247RANDOM64.8
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]
5.381.4-1.9-2.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.566
r_dihedral_angle_3_deg20.616
r_dihedral_angle_4_deg18.105
r_dihedral_angle_1_deg6.176
r_scangle_it1.898
r_angle_refined_deg1.518
r_scbond_it1.102
r_mcangle_it1.013
r_angle_other_deg0.948
r_mcbond_it0.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.566
r_dihedral_angle_3_deg20.616
r_dihedral_angle_4_deg18.105
r_dihedral_angle_1_deg6.176
r_scangle_it1.898
r_angle_refined_deg1.518
r_scbond_it1.102
r_mcangle_it1.013
r_angle_other_deg0.948
r_mcbond_it0.556
r_symmetry_hbond_refined0.403
r_mcbond_other0.327
r_symmetry_vdw_refined0.302
r_symmetry_vdw_other0.251
r_nbd_refined0.216
r_nbd_other0.209
r_xyhbond_nbd_refined0.181
r_xyhbond_nbd_other0.178
r_chiral_restr0.105
r_nbtor_other0.096
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms35292
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms804

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling