2IJF | pdb_00002ijf

Crystal Structure of the Poliovirus RNA-Dependent RNA Polymerase Fidelity Mutant 3Dpol G64S

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RA6	PDB code 1RA6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	2M sodium acetate, 0.1 M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.92	74.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.843	α = 90
b = 125.843	β = 90
c = 113.155	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	IMAGE PLATE	RIGAKU		2006-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3	30			6		20317

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11				4.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 1RA6	3	20	19216	1038	99.61	0.21322	0.21165	0.2	0.24447	0.23	RANDOM	89.24

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]
6.84	3.42		6.84		-10.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.803
r_dihedral_angle_4_deg	7.99
r_dihedral_angle_3_deg	7.888
r_scangle_it	6.422
r_scbond_it	4.407
r_mcangle_it	3.328
r_mcbond_it	2.026
r_angle_refined_deg	1.545
r_dihedral_angle_1_deg	1.435
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.803
r_dihedral_angle_4_deg	7.99
r_dihedral_angle_3_deg	7.888
r_scangle_it	6.422
r_scbond_it	4.407
r_mcangle_it	3.328
r_mcbond_it	2.026
r_angle_refined_deg	1.545
r_dihedral_angle_1_deg	1.435
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.112
r_bond_refined_d	0.01
r_gen_planes_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3697
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	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.