2R70

Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	5% PEG 3350, 0.4M LiNO3, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.801	α = 90
b = 123.801	β = 90
c = 361.843	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 315		2007-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.975	ESRF	ID29

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	107.215	95	0.1	0.1	4.9	12.2	43251	43251

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)
	2.7	2.85	96.3		0.434	0.434	1.7	12.5	6265

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.7	40	43248	43248	2195	93.93	0.223	0.221	0.256	RANDOM	48.396

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]
0.06	0.03		0.06		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.301
r_dihedral_angle_4_deg	20.276
r_dihedral_angle_3_deg	18.554
r_dihedral_angle_1_deg	5.559
r_scangle_it	2.103
r_angle_refined_deg	1.257
r_scbond_it	1.221
r_mcangle_it	0.997
r_mcbond_it	0.558
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.301
r_dihedral_angle_4_deg	20.276
r_dihedral_angle_3_deg	18.554
r_dihedral_angle_1_deg	5.559
r_scangle_it	2.103
r_angle_refined_deg	1.257
r_scbond_it	1.221
r_mcangle_it	0.997
r_mcbond_it	0.558
r_nbtor_refined	0.301
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.087
r_symmetry_hbond_refined	0.041
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5853
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
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.