3EDY

Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5278PEG 6000, citrate, pH 5.0, vapor diffusion, hanging drop, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.448.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.807α = 90
b = 93.173β = 90
c = 102.479γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2007-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.97908NSLSX4C

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
11.835099.10.0797485615089037
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)
11.831.993.10.4572.34.84675

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.8529.724856148127123197.010.1790.1790.205RANDOM26.882
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]
-0.030.13-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.405
r_dihedral_angle_4_deg15.069
r_dihedral_angle_3_deg13.894
r_dihedral_angle_1_deg7.328
r_scangle_it4.871
r_scbond_it3.351
r_mcangle_it2.165
r_mcbond_it1.466
r_angle_refined_deg1.263
r_angle_other_deg1.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.405
r_dihedral_angle_4_deg15.069
r_dihedral_angle_3_deg13.894
r_dihedral_angle_1_deg7.328
r_scangle_it4.871
r_scbond_it3.351
r_mcangle_it2.165
r_mcbond_it1.466
r_angle_refined_deg1.263
r_angle_other_deg1.038
r_mcbond_other0.462
r_symmetry_vdw_other0.291
r_nbd_other0.227
r_nbd_refined0.226
r_nbtor_refined0.191
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.146
r_metal_ion_refined0.135
r_symmetry_hbond_refined0.109
r_nbtor_other0.106
r_chiral_restr0.088
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4195
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms73

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
SOLVEphasing