7H6G | pdb_00007h6g

THE 1.21 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH N-[2-[6-fluoro-2-[(4-hydroxy-5-methyl-2-oxo-5-phenylfuran-3-yl)-phenylmethyl]-1H-indol-3-yl]ethyl]acetamide

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
2.15	42.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.11	α = 90
b = 74.45	β = 90.3
c = 60.65	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 225 mm CCD		2006-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9999	SLS	X06SA

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	1.21	60.63	88.9	0.072	0.078	16.66			117974

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	1.21	1.28		60	0.378	0.432

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	1.21	60.63	112057	5916	88.91	0.15797	0.15677	0.1613	0.18106	0.1843	RANDOM	14.404

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]
-0.22		-0.14	-0.73		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.668
r_dihedral_angle_4_deg	12.831
r_dihedral_angle_3_deg	11.624
r_sphericity_free	6.183
r_dihedral_angle_1_deg	6.146
r_sphericity_bonded	3.181
r_scangle_it	3.071
r_scbond_it	2.428
r_mcangle_it	1.894
r_mcbond_it	1.597
r_angle_refined_deg	1.538
r_rigid_bond_restr	1.292
r_angle_other_deg	0.829
r_mcbond_other	0.627
r_symmetry_vdw_other	0.284
r_nbd_refined	0.193
r_nbd_other	0.192
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.147
r_symmetry_vdw_refined	0.129
r_metal_ion_refined	0.111
r_chiral_restr	0.096
r_nbtor_other	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3621
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	112

Software

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