2OBQ | pdb_00002obq

Discovery of the HCV NS3/4A Protease Inhibitor SCH503034. Key Steps in Structure-Based Optimization

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	The protein (NS3 complexed with KK-NS4a(21-39)-KK peptide) was at 12-15 mg/ml in 15 mM MES, pH 6.5 1 M NaCl 20 mM b-mercaptoethanol. Hanging Drops were formed by mixing 4:l protein solution with 4:l {0.75-1.0 M NaCl, 0.1M Na/K phosphate 0.1 M Mes, pH 5.8-6.1 20 mM b-mercaptoethanol} The drop was equilibrated the drops over 1 ml {(1.25-1.50 M) NaCl - 0.1M Na/K phosphate 0.1 M Mes, pH 5.6-5.8, 20 mM b-mercaptoethanol} , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.57	α = 90
b = 225.57	β = 90
c = 75.72	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

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	2.5	50	89.4	0.066	11.7	1.9	25418	22724		2.3	25.1

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	2.5		76.3		0.276	2.3	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MIR	2.5	8	25418	22724		89.4	0.203	0.264

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
x_angle_deg	1.9
x_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2718
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	2

Software

Software
Software Name	Purpose
ADSC	data collection
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.