Experiment: 2R9M

Cathepsin S complexed with Compound 15

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MS6	pdb entry 1MS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	100mM NaOAc, 18-35% PEG MME (500-8000), 2 M (NH4)2SO4 with or without 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.273	α = 90
b = 85.273	β = 90
c = 150.331	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	RIGAKU RAXIS IIC	Osmic focussing mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.97	50	97	0.161		14.7		38822

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	pdb entry 1MS6	1.97	50	38819	1972		0.175	0.1687	0.208	0.1984	random	13.721

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
x_dihedral_angle_d	24.9
x_angle_deg	1.4
x_improper_angle_d	0.85
x_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3364
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	58

Software

Software
Software Name	Purpose
X-PLOR	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing
CNS	refinement