2P6W | pdb_00002p6w

Crystal structure of a glycosyltransferase involved in the glycosylation of the major capsid of PBCV-1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	50mM socium citrate, 200mM NaCl, 25% PEG3500, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.229	α = 90
b = 63.017	β = 115.42
c = 44.772	γ = 90

Symmetry
Space Group	P 1 21 1

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 RAXIS IV		2006-08-15	M	SINGLE WAVELENGTH
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	30	90.6	0.067	15.3	3.4		31588

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	36.2		0.429		1.7	1256

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.6	8	28206	2812	99.21	0.175	0.172	0.18	0.195	0.21	RANDOM	24.577

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]
1.2		1.44	-0.73		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.003
r_dihedral_angle_4_deg	17.859
r_dihedral_angle_3_deg	10.86
r_dihedral_angle_1_deg	5.671
r_scangle_it	2.557
r_scbond_it	1.783
r_angle_refined_deg	1.397
r_mcangle_it	1.066
r_mcbond_it	0.721
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.003
r_dihedral_angle_4_deg	17.859
r_dihedral_angle_3_deg	10.86
r_dihedral_angle_1_deg	5.671
r_scangle_it	2.557
r_scbond_it	1.783
r_angle_refined_deg	1.397
r_mcangle_it	1.066
r_mcbond_it	0.721
r_nbtor_refined	0.318
r_chiral_restr	0.231
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.15
r_xyhbond_nbd_refined	0.097
r_symmetry_hbond_refined	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1733
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHARP	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.