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Prolyl Tripeptidyl Aminopeptidase Complexed with an Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D5L PDB ENTRY 2D5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 1.1M Potassium Sodium tartrate, 0.2M Lithium Sulfate, 0.1M CHES Buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.29 62.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.103 α = 90 b = 150.103 β = 90 c = 160.985 γ = 120
Symmetry Space Group P 63 2 2
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 QUANTUM 315 monochromator 2006-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.2 50 99.9 0.07 79.2 20.7 54747 39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.277 14 19.8 5385
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2D5L 2.2 20 51058 2718 98.4 0.19 0.188 0.1898 0.231 0.2322 RANDOM 43.1
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] -1.04 -0.52 -1.04 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.74 r_dihedral_angle_4_deg 17.17 r_dihedral_angle_3_deg 14.458 r_dihedral_angle_1_deg 6.94 r_scangle_it 3.953 r_scbond_it 2.774 r_mcangle_it 1.792 r_angle_refined_deg 1.617 r_mcbond_it 1.176 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.74 r_dihedral_angle_4_deg 17.17 r_dihedral_angle_3_deg 14.458 r_dihedral_angle_1_deg 6.94 r_scangle_it 3.953 r_scbond_it 2.774 r_mcangle_it 1.792 r_angle_refined_deg 1.617 r_mcbond_it 1.176 r_nbtor_refined 0.312 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5230 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing