2HCN | pdb_00002hcn

Crystal structure of RNA dependent RNA polymerase domain from west nile virus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HCS	WEST NILE VIRUS RNA DEPENDANT RNA POLYMERASE COORDINATES 2HCS (DOMAIN FROM AMINO ACIDS 317-905)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	10% peg 8000, Imid 0.1M, Ca(OAc)2 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.064	α = 90
b = 110.064	β = 90
c = 68.572	γ = 90

Symmetry
Space Group	P 43

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	MAR CCD 165 mm		2005-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.9330	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	2.35	69	99.9	0.055	21.8	5.7		34338			61.1

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	2.35	2.48	99.7		0.56	1.5	3.5	4930

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 (All)	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	WEST NILE VIRUS RNA DEPENDANT RNA POLYMERASE COORDINATES 2HCS (DOMAIN FROM AMINO ACIDS 317-905)	2.35	34.82	34348	32583	1734	99.92	0.20962	0.20962	0.20701	0.2	0.25944	0.26	RANDOM	58.568

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]
-1.96			-1.96		3.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.388
r_dihedral_angle_3_deg	20.655
r_dihedral_angle_4_deg	19.044
r_dihedral_angle_1_deg	7.286
r_scangle_it	2.747
r_scbond_it	1.827
r_angle_refined_deg	1.729
r_mcangle_it	1.255
r_mcbond_it	0.728
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.151
r_metal_ion_refined	0.022
r_bond_refined_d	0.021
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3931
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
AMoRE	phasing