6YYN

Structure of Cathepsin S in complex with Compound 14

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished isomorphous structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	285	0.1 M sodium citrate pH 4.8, 0.2 M ammonium sulfate, 17% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.671	α = 90
b = 85.671	β = 90
c = 150.922	γ = 90

Symmetry
Space Group	P 41 2 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	MAR scanner 345 mm plate		2014-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.22	19.51	99.4	0.118	0.058	0.994	10.1	3.9		28281

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.34	99.8		0.68	0.344	0.732	2.5	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	unpublished isomorphous structure	2.22	19.51	28263	1436	99.005	0.161	0.1581	0.217	33.279

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]
0.171			0.171		-0.341

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.126
r_dihedral_angle_4_deg	16.093
r_dihedral_angle_3_deg	14.208
r_dihedral_angle_1_deg	6.998
r_lrange_it	6.963
r_lrange_other	6.868
r_scangle_it	2.99
r_scangle_other	2.99
r_mcangle_it	2.137
r_mcangle_other	2.137
r_scbond_other	2.037
r_scbond_it	2.034
r_angle_refined_deg	1.741
r_angle_other_deg	1.624
r_mcbond_it	1.319
r_mcbond_other	1.319
r_nbd_other	0.257
r_symmetry_nbd_refined	0.217
r_xyhbond_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.201
r_nbd_refined	0.195
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.178
r_ncsr_local_group_1	0.104
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.013
r_bond_other_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3447
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing