2EC0 | pdb_00002ec0

RNA-dependent RNA polymerase of foot-and-mouth disease virus in complex with a template-primer RNA and ATP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U09	PDB ENTRY 1U09

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	30% PEG 4000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.656	α = 90
b = 95.656	β = 90
c = 201.458	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	197	CCD	ADSC QUANTUM 4		2004-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93	ESRF	ID14-2

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	2.7	30	95	0.075	0.054	7.6		30133	28495	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	PDB ENTRY 1U09	2.75	20	2	2	23062	1223	85.49	0.24741	0.24486	0.28	0.29548	0.32	RANDOM	52.027

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]
0.35	0.18		0.35		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.805
r_dihedral_angle_3_deg	17.703
r_dihedral_angle_4_deg	16.264
r_dihedral_angle_1_deg	4.968
r_scangle_it	1.37
r_angle_refined_deg	1.15
r_scbond_it	0.808
r_mcangle_it	0.761
r_mcbond_it	0.422
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.805
r_dihedral_angle_3_deg	17.703
r_dihedral_angle_4_deg	16.264
r_dihedral_angle_1_deg	4.968
r_scangle_it	1.37
r_angle_refined_deg	1.15
r_scbond_it	0.808
r_mcangle_it	0.761
r_mcbond_it	0.422
r_nbtor_refined	0.303
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.08
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7428
Nucleic Acid Atoms	638
Solvent Atoms	114
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.