4OBC

Crystal structure of HCV polymerase NS5b genotype 2a JFH-1 isolate with the S15G, C223H, V321I resistance mutations against the guanosine analog GS-0938 (PSI-3529238)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	NS5b VCID 5854 at 4.25 mg/mL in 5 mM Tris pH 7.5, 200 mM NH4OAc, 1 mM EDTA 1 mM DTT against PACT screen condition D5, 25% PEG 1500, 0.1M MMT Malic Acid, MES, Tris Buffer pH 8.0 supplemented with 20% glycerol as cryo-protectant, crystal tracking ID 223572d5, puck ID cps0237-1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.208	α = 90
b = 140.208	β = 90
c = 92.567	γ = 120

Symmetry
Space Group	P 65

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 325 mm CCD		2011-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	2.5	50	99.7	0.085	21.9	7.8		35841

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	2.5	2.57	97.3		0.638	2.3	3.7	2877

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 1YUY	2.5	50	35745	1792	99.58	0.1899	0.1882	0.2234	RANDOM	39.3253

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]
1.88	0.94		1.88		-2.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.85
r_dihedral_angle_3_deg	15.998
r_dihedral_angle_4_deg	14.859
r_dihedral_angle_1_deg	5.848
r_scangle_it	3.585
r_scbond_it	2.1
r_mcangle_it	1.452
r_angle_refined_deg	1.421
r_mcbond_it	0.741
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.85
r_dihedral_angle_3_deg	15.998
r_dihedral_angle_4_deg	14.859
r_dihedral_angle_1_deg	5.848
r_scangle_it	3.585
r_scbond_it	2.1
r_mcangle_it	1.452
r_angle_refined_deg	1.421
r_mcbond_it	0.741
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4277
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.