1BGO | pdb_00001bgo

CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.95	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.55	α = 90
b = 71.55	β = 90
c = 55.09	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	287	AREA DETECTOR	XENTRONICS		1997-09-17	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	SIEMENS

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	35	89	0.089	0.089	12.4	3.6		11258		2	28.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.4	54		0.27	0.27	1.8	1.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	1ATK	2.3	8	2	9666	1016	79.3	0.24	0.24	0.296	RANDOM	15

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
x_dihedral_angle_d	25.2
x_angle_deg	1.9
x_improper_angle_d	1.82
x_bond_d	0.017
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1698
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	34

Software

Software
Software Name	Purpose
XENGEN	data collection
CCP4	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
CCP4	data scaling
X-PLOR	phasing