6IC7 | pdb_00006ic7

Human cathepsin-C in complex with dipeptidyl cyclopropyl nitrile inhibitor 3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20.0 % (w/v) PEG 3000 0.2 M ammonium citrate dibasic 2.5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.365	α = 90
b = 87.549	β = 90
c = 115.004	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	Bruker Platinum 135		2010-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.5418

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	2	28.3	98.2	0.069	23.8	11.5		30537

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	2	2.1	85.5		0.164	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	2	28.231	29338	1466	97.252	0.162	0.1596	0.1708	0.2034	0.2125	20.023

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]
0.146			0.417		-0.563

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.536
r_dihedral_angle_4_deg	23.757
r_dihedral_angle_1_deg	19.05
r_dihedral_angle_3_deg	14.674
r_lrange_other	5.601
r_lrange_it	5.599
r_dihedral_angle_other_3_deg	4.877
r_mcangle_it	2.349
r_mcangle_other	2.349
r_scangle_it	2.225
r_scangle_other	2.225
r_angle_refined_deg	1.931
r_angle_other_deg	1.462
r_mcbond_it	1.396
r_mcbond_other	1.395
r_scbond_it	1.358
r_scbond_other	1.358
r_symmetry_xyhbond_nbd_refined	0.33
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.229
r_nbd_other	0.216
r_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.184
r_symmetry_nbtor_other	0.093
r_symmetry_xyhbond_nbd_other	0.093
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	127

Software

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