6YYR | pdb_00006yyr

Structure of Cathepsin S in complex with Compound 20b

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experimental model	Other		unpublished isomorphous structure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	277	0.10 M sodium citrate pH 4.8, 0.2 M ammonium sulfate, 29% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.84	α = 90
b = 85.84	β = 90
c = 151.9	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	PIXEL	DECTRIS PILATUS 6M-F		2017-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.3	30	93.6	0.063	0.022	0.999	16.6	8		129490

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	1.3	1.37	96.4		0.707	0.256	0.748	2.8	7.3

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X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	unpublished isomorphous structure	1.3	29.779	129488	6484	92.89	0.098	0.0966	0.1	0.1306	0.13	15.978

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]
0.006			0.006		-0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.365
r_dihedral_angle_4_deg	16.031
r_dihedral_angle_1_deg	14.145
r_dihedral_angle_3_deg	11.846
r_dihedral_angle_other_3_deg	10.551
r_lrange_it	4.882
r_lrange_other	4.063
r_rigid_bond_restr	3.999
r_scbond_it	3.317
r_scbond_other	3.317
r_scangle_it	3.288
r_scangle_other	3.288
r_angle_refined_deg	2.18
r_mcangle_it	1.706
r_mcangle_other	1.706
r_angle_other_deg	1.646
r_mcbond_it	1.419
r_mcbond_other	1.418
r_symmetry_nbd_refined	0.268
r_nbd_other	0.263
r_chiral_restr	0.252
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.221
r_xyhbond_nbd_refined	0.2
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.185
r_symmetry_nbtor_other	0.093
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3428
Nucleic Acid Atoms
Solvent Atoms	878
Heterogen Atoms	135

Software

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