2DJG

Re-determination of the native structure of human dipeptidyl peptidase I (cathepsin C)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K3B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42981.8M ammonium sulfate, 0.1M Na citrate, 0.2M Na/K tartrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.856.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.479α = 90
b = 88.68β = 90
c = 114.35γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 345 mm plate2004-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0530120690120690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1296.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1k3b2.0524.042578725787137696.110.176120.176120.173750.22076RANDOM23.055
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.872
r_scangle_it4.066
r_scbond_it2.66
r_mcangle_it1.993
r_angle_refined_deg1.849
r_mcbond_it1.115
r_angle_other_deg0.978
r_symmetry_vdw_other0.264
r_nbd_other0.256
r_nbd_refined0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.872
r_scangle_it4.066
r_scbond_it2.66
r_mcangle_it1.993
r_angle_refined_deg1.849
r_mcbond_it1.115
r_angle_other_deg0.978
r_symmetry_vdw_other0.264
r_nbd_other0.256
r_nbd_refined0.239
r_xyhbond_nbd_refined0.185
r_symmetry_hbond_refined0.15
r_chiral_restr0.137
r_symmetry_vdw_refined0.131
r_nbtor_other0.09
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2720
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling