7H6H | pdb_00007h6h

THE 1.94 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH 1-[(7-fluoronaphthalen-1-yl)methyl]-3-[[methoxycarbonyl(methyl)amino]methyl]indole-2-carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	293	0.2 M LiSO4 (Salt), 25 %w/v PEG3350 (Precipitant), 0.1 M HEPES 7.5 pH (Buffer), Protein was at 17 mg/mL.

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.21	α = 90
b = 44.73	β = 107.08
c = 67.27	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	MAR scanner 345 mm plate		2006-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.94	19.51	89.9	0.08	0.091	14.83			15390

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	2.06		89.9	0.398	0.455

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.94	19.51	14611	779	90.02	0.17363	0.1706	0.1774	0.23162	0.2351	RANDOM	19.85

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]
-0.4		0.44	0.49		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.662
r_dihedral_angle_1_deg	6.701
r_long_range_B_refined	5.68
r_long_range_B_other	5.233
r_dihedral_angle_2_deg	4.256
r_scangle_other	1.197
r_angle_refined_deg	1.181
r_mcangle_it	0.867
r_mcangle_other	0.867
r_scbond_it	0.73
r_scbond_other	0.721
r_mcbond_it	0.496
r_mcbond_other	0.494
r_angle_other_deg	0.425
r_chiral_restr	0.061
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1786
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	42

Software

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