3OVX | pdb_00003ovx

Cathepsin S in complex with a covalent inhibitor with an aldehyde warhead

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	soaking cat S crystals	5	298	Composition of crystallisation solution (including components from protein prep) 50 mM NaAcetate; 0.25 M NaCl; 4 mM MMTS: 26% PEG 4K; 0.1 M NaCitrate pH=5.0; 0,2 M (NH4)2SO4; 10 mM DMSO; 10 mM DTT Crystallisation method and temperature Hanging drop; RT Cryoprotectant composition 30% PEG 4K, 0.1 M NaCitrate pH=5.0; 0.2 M (NH4)2SO4; 15% PEG 400 (+ 10% compound) , soaking cat S crystals, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.545	α = 90
b = 85.545	β = 90
c = 150.571	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		CCD	RAXIS-IV++		2008-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	1.49	74.38	89.8	0.082				83072		1.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	In-house cathepsin S structure	1.49	74.38	78873	4178	89.81	0.20168	0.20037	0.2	0.22614	0.23	RANDOM	13.608

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.881
r_dihedral_angle_4_deg	19.41
r_dihedral_angle_3_deg	12.044
r_dihedral_angle_1_deg	5.423
r_scangle_it	2.736
r_scbond_it	2.003
r_angle_refined_deg	1.195
r_mcangle_it	1.054
r_mcbond_it	0.908
r_angle_other_deg	0.833
r_symmetry_vdw_other	0.33
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.202
r_nbd_other	0.19
r_nbtor_refined	0.18
r_mcbond_other	0.177
r_symmetry_hbond_refined	0.116
r_xyhbond_nbd_refined	0.103
r_nbtor_other	0.083
r_chiral_restr	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3372
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	42

Software

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