2R72

Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	10% PEG 3350, 0.4M LiNO3, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.838	α = 90
b = 122.838	β = 90
c = 354.255	γ = 120

Symmetry
Space Group	P 61 2 2

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	ADSC QUANTUM 4		2006-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	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	3.15	36.664	98.4	0.121	0.121	5.1	6.5	27660	27660

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	3.15	3.32	98.6		0.356	0.356	1.9	4.2	3962

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2PUS	3.15	20	27545	27545	1393	97.5	0.211	0.209	0.235	RANDOM	63.897

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]
-0.34	-0.17		-0.34		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.265
r_dihedral_angle_4_deg	18.041
r_dihedral_angle_3_deg	16.509
r_dihedral_angle_1_deg	4.716
r_angle_refined_deg	0.962
r_scangle_it	0.807
r_mcangle_it	0.504
r_scbond_it	0.447
r_nbtor_refined	0.297
r_mcbond_it	0.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.265
r_dihedral_angle_4_deg	18.041
r_dihedral_angle_3_deg	16.509
r_dihedral_angle_1_deg	4.716
r_angle_refined_deg	0.962
r_scangle_it	0.807
r_mcangle_it	0.504
r_scbond_it	0.447
r_nbtor_refined	0.297
r_mcbond_it	0.279
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.142
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.065
r_symmetry_hbond_refined	0.045
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5915
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.