2DJG

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K3B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	1.8M ammonium sulfate, 0.1M Na citrate, 0.2M Na/K tartrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.08

Crystal Data

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

Symmetry
Space Group	I 2 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	120	IMAGE PLATE	MAR scanner 345 mm plate		2004-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	30				120690	120690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	96.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1k3b	2.05	24.04	25787	25787	1376	96.11	0.17612	0.17612	0.17375	0.22076	RANDOM	23.055

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
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.872
r_scangle_it	4.066
r_scbond_it	2.66
r_mcangle_it	1.993
r_angle_refined_deg	1.849
r_mcbond_it	1.115
r_angle_other_deg	0.978
r_symmetry_vdw_other	0.264
r_nbd_other	0.256
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.185
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.137
r_symmetry_vdw_refined	0.131
r_nbtor_other	0.09
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.002
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 Atoms	Number
Protein Atoms	2720
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling