6YYQ | pdb_00006yyq

Structure of Cathepsin S in complex with Compound 3

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experimental model	Other		unpublished isomorphous structure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, SITTING DROP	7.3	285	0.2 M potassium formate pH 7.3, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.765	α = 90
b = 92.765	β = 90
c = 182.893	γ = 120

Symmetry
Space Group	P 32 2 1

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	2.51	28.82	99.8	0.096	0.037	0.998	11.9	6.5		31846

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	2.51	2.65	99.9		0.623	0.232	0.913	2.6	6.9

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X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	unpublished isomorphous structure	2.51	28.82	31800	1599	99.743	0.213	0.2098	0.21	0.2802	0.28	74.379

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]
1.776	0.888		1.776		-5.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.737
r_dihedral_angle_3_deg	18.151
r_dihedral_angle_4_deg	14.41
r_dihedral_angle_1_deg	7.031
r_lrange_it	6.523
r_lrange_other	6.513
r_mcangle_other	3.321
r_mcangle_it	3.32
r_scangle_it	3.274
r_scangle_other	3.274
r_mcbond_it	2.109
r_mcbond_other	2.105
r_scbond_it	1.999
r_scbond_other	1.999
r_angle_refined_deg	1.546
r_angle_other_deg	1.286
r_symmetry_nbd_refined	0.288
r_symmetry_xyhbond_nbd_refined	0.254
r_nbd_other	0.245
r_xyhbond_nbd_refined	0.21
r_nbd_refined	0.206
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_other	0.11
r_ncsr_local_group_6	0.104
r_ncsr_local_group_5	0.103
r_ncsr_local_group_3	0.099
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_ncsr_local_group_2	0.07
r_ncsr_local_group_1	0.069
r_ncsr_local_group_4	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6892
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	51

Software

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