1DY9

Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (inhibitor I)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY7	PDB ENTRY 1DY7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.1		THE NS3 PROTEIN (1MG/ML) WAS INCUBATE AT 4C WITH THE NS4A COFACTOR PEPTIDE, CONTAINING A SOLUBIZING LYSINE TAG AT ITS N- AND C-TERMINI(KGSVVIVGRIILSGRK), AT A MOLAR RATIO OF 1:2 AND CONCENTRATED TO 290 MICROMOLAR. NS3J/4A CRYSTALS, WITH A MAXIMUM SIZE OF 0.6 X 0.3 X 0.2 MM**3, WERE OBTAINED BY BOTH HANGING- AND SITTING-DROP VAPOUR DIFFUSION METHODS AFTER TWO WEEKS AT ROOM TEMPERATURE, WITH 3.4 M NACL, 10MM DTT, 0.1 M CITRATE BUFFER PH 5.1. THE TERNARY COMPLEX WITH INHIBITOR WAS PREPARED BY ADDING 5.0 MM OF INIBITOR TO CRYSTALS THAT WERE STABILISED IN 4.5 M NACL, 10 MM DTT, 0.1 M CITRATE BUFFER, PH 5.1.

Crystal Properties
Matthews coefficient	Solvent content
2.37	47.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.35	α = 90
b = 94.35	β = 90
c = 82.37	γ = 120

Symmetry
Space Group	P 61

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	MARRESEARCH	TOROIDAL MIRROR	1999-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	20	98.2	0.035	32	2.8		23960		-3	37.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	98.4		0.15	3.2	2.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DY7	2.1	20	23960	1224	98.2	0.207	0.213	0.275	RANDOM	43.5

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	26.4
p_staggered_tor	20.5
p_planar_tor	6.7
p_scangle_it	5.49
p_mcangle_it	4.18
p_scbond_it	3.77
p_mcbond_it	2.9
p_multtor_nbd	0.278
p_xyhbond_nbd	0.201
p_singtor_nbd	0.193
p_chiral_restr	0.125
p_angle_d	0.03
p_planar_d	0.03
p_plane_restr	0.012
p_bond_d	0.01
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2734
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing