3O0U

Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG

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	VAPOR DIFFUSION, HANGING DROP	3.9	298	8% PEG 4K, 0.2 M Ammonium Sulfate pH=3.9, 4% Methanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.695	α = 90
b = 48.967	β = 90
c = 103.958	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH		2006-06-15	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)	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	1.8	51.988	100	0.053			10838	10838	1.9	1.9

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)
	1.8	1.86	16.1		0.133	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	In-house cathepsin K structure	1.8	51.988	1.9	10322	516	58.59	0.15512	0.15201	0.2168	RANDOM	12.813

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]
-0.19			0.12		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.565
r_dihedral_angle_3_deg	17.069
r_dihedral_angle_4_deg	16.694
r_dihedral_angle_1_deg	5.396
r_scangle_it	2.469
r_scbond_it	1.787
r_angle_refined_deg	1.431
r_mcangle_it	1.035
r_angle_other_deg	0.904
r_mcbond_it	0.842
r_symmetry_vdw_other	0.295
r_nbd_refined	0.222
r_nbd_other	0.203
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.172
r_mcbond_other	0.168
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.085
r_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
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	1649
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	26

Software

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