3OVZ

Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		In-house cathepsin K structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			298	0 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20% PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.741	α = 90
b = 55.741	β = 90
c = 128.916	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2008-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.02	55.74	100				14051

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	2.02	2.09	100		0.7	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	In-house cathepsin K structure	2.02	51.16	13991	698	99.7	0.247	0.244	0.308	35.26

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]
0.99			0.99		-1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.592
r_dihedral_angle_3_deg	18.138
r_dihedral_angle_4_deg	13.198
r_dihedral_angle_1_deg	6.198
r_scangle_it	2.502
r_scbond_it	1.891
r_angle_refined_deg	1.785
r_mcangle_it	1.106
r_angle_other_deg	1.052
r_mcbond_it	0.917
r_symmetry_vdw_other	0.3
r_symmetry_vdw_refined	0.276
r_symmetry_hbond_refined	0.257
r_nbd_refined	0.215
r_nbd_other	0.211
r_nbtor_refined	0.187
r_mcbond_other	0.171
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.104
r_nbtor_other	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1637
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	40

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling