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Crystal structure of HIV-1 Tat derived nonapeptides Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N1M PDB ENTRY 1N1M
Crystallization Crystal Properties Matthews coefficient Solvent content 2.61 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.299 α = 90 b = 127.043 β = 90 c = 137.332 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2004-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 30 92 0.07 19.8 4.3 127470 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 87.7 0.37 3.1 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1N1M 2 30 2 127470 1297 92.1 0.16 0.16 0.203 0.3067 RANDOM 38.7
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 -0.11 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.012 r_dihedral_angle_4_deg 18.887 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_1_deg 6.384 r_scangle_it 3.048 r_scbond_it 2.066 r_angle_refined_deg 1.508 r_mcbond_it 1.041 r_angle_other_deg 0.858 r_symmetry_hbond_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.012 r_dihedral_angle_4_deg 18.887 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_1_deg 6.384 r_scangle_it 3.048 r_scbond_it 2.066 r_angle_refined_deg 1.508 r_mcbond_it 1.041 r_angle_other_deg 0.858 r_symmetry_hbond_refined 0.233 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_other 0.209 r_nbd_refined 0.207 r_mcangle_it 0.203 r_nbd_other 0.189 r_chiral_restr 0.15 r_symmetry_vdw_refined 0.129 r_nbtor_other 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 11990 Nucleic Acid Atoms Solvent Atoms 1746 Heterogen Atoms 364
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing