2BGR

Crystal structure of HIV-1 Tat derived nonapeptides 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 1N1MPDB ENTRY 1N1M

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.6152.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.299α = 90
b = 127.043β = 90
c = 137.332γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-05-03MSINGLE 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
1230920.0719.84.31274702
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)
122.0787.70.373.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1N1M2302127470129792.10.160.160.203RANDOM38.7
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]
-1.49-0.111.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.012
r_dihedral_angle_4_deg18.887
r_dihedral_angle_3_deg14.58
r_dihedral_angle_1_deg6.384
r_scangle_it3.048
r_scbond_it2.066
r_angle_refined_deg1.508
r_mcbond_it1.041
r_angle_other_deg0.858
r_symmetry_hbond_refined0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.012
r_dihedral_angle_4_deg18.887
r_dihedral_angle_3_deg14.58
r_dihedral_angle_1_deg6.384
r_scangle_it3.048
r_scbond_it2.066
r_angle_refined_deg1.508
r_mcbond_it1.041
r_angle_other_deg0.858
r_symmetry_hbond_refined0.233
r_xyhbond_nbd_refined0.215
r_symmetry_vdw_other0.209
r_nbd_refined0.207
r_mcangle_it0.203
r_nbd_other0.189
r_chiral_restr0.15
r_symmetry_vdw_refined0.129
r_nbtor_other0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_refined
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_mcbond_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 Atoms11990
Nucleic Acid Atoms
Solvent Atoms1746
Heterogen Atoms364

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing