3BSN | pdb_00003bsn

Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SH0	pdb entry 1SH0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	16% (w/v) PEG 8000, 25% (w/v) glycerol, 100 mM Tris-HCl, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM 2-mercaptoethanol, 0.1% (w/v) CHAPS, 0.5 mM RNA duplex, 1 mM NTP, 0.03 mM polymerase, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.31	α = 90
b = 93.85	β = 90
c = 96.03	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	CCD	MARMOSAIC 225 mm CCD	White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)	2007-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	30	93.6	0.079	0.079	13.7	4.8	58959	58959	-3	-3	24.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.97	78.3		0.614	0.614	2.3	4.3	11566

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	pdb entry 1SH0	1.8	19.71	58959	58754	2989	93.3	0.20251	0.20251	0.20069	0.2	0.23585	0.23	RANDOM	32.254

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]
3.09			-0.86		-2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.599
r_dihedral_angle_4_deg	17.96
r_dihedral_angle_3_deg	12.972
r_scangle_it	4.884
r_dihedral_angle_1_deg	4.876
r_scbond_it	3.574
r_mcangle_it	2.576
r_mcbond_it	1.845
r_angle_refined_deg	1
r_nbtor_refined	0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.599
r_dihedral_angle_4_deg	17.96
r_dihedral_angle_3_deg	12.972
r_scangle_it	4.884
r_dihedral_angle_1_deg	4.876
r_scbond_it	3.574
r_mcangle_it	2.576
r_mcbond_it	1.845
r_angle_refined_deg	1
r_nbtor_refined	0.291
r_nbd_refined	0.176
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_refined	0.099
r_symmetry_hbond_refined	0.088
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3762
Nucleic Acid Atoms	361
Solvent Atoms	347
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	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.