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Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 278 PEG 6000, citrate, pH 5.0, vapor diffusion, hanging drop, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.807 α = 90 b = 93.173 β = 90 c = 102.479 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2007-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97908 NSLS X4C
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 1.83 50 99.1 0.079 7 48561 50890 37
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 1.83 1.9 93.1 0.457 2.3 4.8 4675
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 1.85 29.72 48561 48127 1231 97.01 0.179 0.179 0.1975 0.205 0.2155 RANDOM 26.882
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] -0.03 0.13 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.405 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 7.328 r_scangle_it 4.871 r_scbond_it 3.351 r_mcangle_it 2.165 r_mcbond_it 1.466 r_angle_refined_deg 1.263 r_angle_other_deg 1.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.405 r_dihedral_angle_4_deg 15.069 r_dihedral_angle_3_deg 13.894 r_dihedral_angle_1_deg 7.328 r_scangle_it 4.871 r_scbond_it 3.351 r_mcangle_it 2.165 r_mcbond_it 1.466 r_angle_refined_deg 1.263 r_angle_other_deg 1.038 r_mcbond_other 0.462 r_symmetry_vdw_other 0.291 r_nbd_other 0.227 r_nbd_refined 0.226 r_nbtor_refined 0.191 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.146 r_metal_ion_refined 0.135 r_symmetry_hbond_refined 0.109 r_nbtor_other 0.106 r_chiral_restr 0.088 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4195 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 73
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection SOLVE phasing