4DMY

Cathepsin K inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	PEG, pH 5.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.927	α = 90
b = 69.554	β = 99.83
c = 90.645	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD	Rh coated meridionally focussing mirror	2006-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.90005	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.63	54.9	97.5	0.079	11	3.2	47594	47594			19.978

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.7	87.7		0.354		2.8	5060

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.63	54.88	47594	45211	2380	97.89	0.1301	0.13086	0.12774	0.19008	RANDOM	13.735

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]
0.03		-0.51	1.49		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.971
r_dihedral_angle_3_deg	12.954
r_dihedral_angle_4_deg	12.154
r_sphericity_free	10.218
r_scangle_it	5.99
r_dihedral_angle_1_deg	5.227
r_scbond_it	5.014
r_sphericity_bonded	4.197
r_mcangle_it	3.554
r_mcbond_it	2.984
r_rigid_bond_restr	2.543
r_mcbond_other	1.272
r_angle_refined_deg	1.219
r_angle_other_deg	0.937
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.208
r_nbd_other	0.19
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.152
r_symmetry_vdw_other	0.151
r_nbtor_other	0.084
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3298
Nucleic Acid Atoms
Solvent Atoms	500
Heterogen Atoms	86

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling