Experiment: 1YT7

Cathepsin K complexed with a constrained ketoamide inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q6K	PDB ENTRY 1Q6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.2M AMMONIUM SULFATE, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.86	31.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.645	α = 90
b = 65.645	β = 90
c = 34.467	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS II		2001-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.3	18.24	96	0.045	18.7	2	7170	7078	1	1	14.4

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)
	2.3	2.44	91.1		0.1	8.8	2	1003

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	PDB ENTRY 1Q6K	2.3	18	1	1	7170	7078	770	96	0.183	0.1861	0.251	0.1801	random	18.4

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]
-2.61	1.54		-2.61		5.22

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.8
c_angle_deg	1.4
c_improper_angle_d	0.78
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1634
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	51

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing