6IC6

Human cathepsin-C in complex with cyclopropyl peptidyl nitrile inhibitor 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	20.0 % (w/v) PEG 6000 0.1 M sodium citrate pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.69	α = 90
b = 87.77	β = 90
c = 115.03	γ = 90

Symmetry
Space Group	I 2 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	MARMOSAIC 225 mm CCD		2009-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.03796	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.898	28.026	97.2	0.05	18.4	3.7		34042

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.898	1.95	96		0.394	3.4

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	in-house structure	1.898	28.026	34042	1684	97.18	0.149	0.147	0.1858	27.472

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]
0.39			1.623		-2.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.483
r_dihedral_angle_4_deg	23.378
r_dihedral_angle_3_deg	13.309
r_dihedral_angle_1_deg	9.377
r_lrange_it	5.593
r_lrange_other	5.593
r_scangle_it	2.735
r_scangle_other	2.735
r_mcangle_it	2.474
r_mcangle_other	2.474
r_angle_refined_deg	1.843
r_scbond_it	1.728
r_scbond_other	1.728
r_mcbond_it	1.581
r_mcbond_other	1.581
r_angle_other_deg	1.451
r_symmetry_nbd_refined	0.299
r_nbd_other	0.243
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_other	0.132
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2760
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	118

Software

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