3GYN | pdb_00003gyn

Crystal structure of HCV NS5B polymerase with a novel monocyclic dihydropyridinone inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		HCV POLYMERASE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	298	20% PEG 4K, 50 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 5 MM DTT, TRANSFERRED TO PH 7.6 FOR SOAKING, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.864	α = 90
b = 106.391	β = 90
c = 126.567	γ = 90

Symmetry
Space Group	P 21 21 21

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	RIGAKU RAXIS IV	mirrors	1997-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.15	34.15	100	0.158	13.6	7.9	63836	63836

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)
	2.15	2.23	100		0.959	1.93	7.6	6262

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	HCV POLYMERASE	2.15	34.15	63740	63740	3231	99.7	0.22771	0.22523	0.23	0.27574	0.28	RANDOM	44.256

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]
			1.31		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.996
r_dihedral_angle_3_deg	13.018
r_dihedral_angle_4_deg	11.859
r_dihedral_angle_1_deg	5.382
r_scangle_it	2.155
r_mcangle_it	1.69
r_scbond_it	1.544
r_mcbond_it	1.117
r_angle_refined_deg	1.027
r_nbtor_refined	0.292
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.186
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8668
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	72

Software

Software
Software Name	Purpose
CrystalClear	data collection
EPMR	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling