6YYO | pdb_00006yyo

Structure of Cathepsin S in complex with Compound 1

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experimental model	Other		unpublished isomorphous structure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	4.2	285	0.1 M sodium citrate pH 4.2, 0.2 M ammonium sulfate and 20 % w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.458	α = 90
b = 85.458	β = 90
c = 150.899	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	CCD	ADSC QUANTUM 315r		2014-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97620	ESRF	ID14-4

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	1.5	28.46	98	0.063	0.031	0.999	13.3	3.7		87701

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	1.5	1.58	99.5		0.627	0.314	0.721	2.7	3.7

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X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	unpublished isomorphous structure	1.5	28.296	87554	4406	97.347	0.139	0.1373	0.14	0.1689	0.17	18.782

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]
-0.119			-0.119		0.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.076
r_dihedral_angle_4_deg	15.33
r_dihedral_angle_3_deg	11.976
r_lrange_it	6.938
r_lrange_other	6.652
r_dihedral_angle_1_deg	6.381
r_scangle_it	2.634
r_scangle_other	2.633
r_angle_refined_deg	1.998
r_scbond_it	1.805
r_scbond_other	1.802
r_angle_other_deg	1.575
r_mcangle_other	1.444
r_mcangle_it	1.443
r_mcbond_it	0.889
r_mcbond_other	0.889
r_symmetry_nbd_refined	0.278
r_nbd_other	0.265
r_symmetry_xyhbond_nbd_other	0.24
r_xyhbond_nbd_refined	0.239
r_symmetry_xyhbond_nbd_refined	0.235
r_nbd_refined	0.222
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.182
r_chiral_restr	0.122
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3426
Nucleic Acid Atoms
Solvent Atoms	688
Heterogen Atoms	203

Software

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