Experiment: 1DEU

CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WITH THE PROREGION COVALENTLY LINKED TO THE ACTIVE SITE CYSTEINE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HUC	Cathepsin B (PDB code 1HUC), Reference: Musil et al EMBO.J 1991, 10, 2321-2330

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	292	300 mM (NH4)2SO4, 12% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.82	α = 90
b = 84.82	β = 90
c = 169.72	γ = 120

Symmetry
Space Group	P 32 2 1

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		1999-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C		NSLS	X8C

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	1.7	45	95.4	0.048	19.5	3.5	521645	82047		0.3	16.4

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	1.7	1.78	90.7		0.208		1.5	7673

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Cathepsin B (PDB code 1HUC), Reference: Musil et al EMBO.J 1991, 10, 2321-2330	1.7	45	1	2	82047	74610	1849	95.1	0.204	0.2076	0.215	0.2196	RANDOM	20.7

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	24.7
c_dihedral_angle_d	24.2
c_angle_deg	2.5
c_scangle_it	1.08
c_mcangle_it	0.98
c_improper_angle_d	0.71
c_scbond_it	0.67
c_mcbond_it	0.55
c_bond_d	0.034

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4193
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms

Software

Software
Software Name	Purpose
Adxv	data processing
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement