2HH5

Crystal Structure of Cathepsin S in complex with a Zinc mediated non-covalent arylaminoethyl amide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F1G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.2M ZnAcetate, 20% PEG-3350, 150mM Sodium Chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.542	α = 90
b = 109.542	β = 90
c = 98.529	γ = 120

Symmetry
Space Group	H 3

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	ADSC QUANTUM 4		2003-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	34.2	99.3	0.064	0.064	17.7	2.7	38549	38549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	98.2		0.763	0.763	1.3	2.5	4514

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2F1G	1.8	34.2	38549	38549	2048	99.34	0.1757	0.17567	0.17328	0.22015	RANDOM	27.905

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]
-0.72	-0.36		-0.72		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.744
r_dihedral_angle_4_deg	12.584
r_dihedral_angle_3_deg	12.197
r_dihedral_angle_1_deg	6.018
r_scangle_it	4.303
r_scbond_it	3.349
r_mcangle_it	1.713
r_angle_refined_deg	1.511
r_mcbond_it	1.425
r_angle_other_deg	0.765
r_mcbond_other	0.3
r_symmetry_vdw_refined	0.283
r_symmetry_vdw_other	0.234
r_nbd_refined	0.201
r_nbtor_refined	0.191
r_nbd_other	0.18
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.134
r_metal_ion_refined	0.114
r_symmetry_metal_ion_refined	0.109
r_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3372
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
PROCESS	data reduction
HKL-2000	data scaling
MOLREP	phasing