6YYP | pdb_00006yyp

Structure of Cathepsin S in complex with Compound 2

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experimental model	Other		unpublished isomorphous structure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	6.8	285	54% v/v tacsimate pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.689	α = 90
b = 118.689	β = 90
c = 205.586	γ = 120

Symmetry
Space Group	H 3 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	PIXEL	DECTRIS PILATUS 6M		2013-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	ESRF	ID29

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	2.05	30	98.7	0.135	0.066	0.99	7.4	3.9		34644

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	2.05	2.16	99.4		0.663	0.32	0.632	2.5	4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	unpublished isomorphous structure	2.05	29.691	34643	1708	98.089	0.144	0.1415	0.15	0.1877	0.19	31.859

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]
0.301	0.15		0.301		-0.975

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.111
r_dihedral_angle_4_deg	17.752
r_dihedral_angle_3_deg	14.491
r_dihedral_angle_1_deg	6.793
r_lrange_it	6.682
r_lrange_other	6.588
r_scangle_it	3.603
r_scangle_other	3.602
r_scbond_it	2.288
r_scbond_other	2.287
r_mcangle_it	1.997
r_mcangle_other	1.996
r_angle_refined_deg	1.73
r_angle_other_deg	1.453
r_mcbond_it	1.327
r_mcbond_other	1.302
r_symmetry_xyhbond_nbd_refined	0.379
r_symmetry_nbd_refined	0.248
r_nbd_other	0.217
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.177
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3448
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	66

Software

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