2ICX | pdb_00002icx

Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapor diffusion, hanging drop with micro-seeding		273	Protein solution (10 mg/ml protein, 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M Tris PH 8.0) mixed in a 1:1 ratio with Well solution ( 28 % PEG 2K, 5% DMSO, 0.10 M MES/Acetate pH 5.5), crystals soaked in well solution supplemented with 0.002 M UTP, vapor diffusion, hanging drop with micro-seeding, temperature 273K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.683	α = 90
b = 59.679	β = 100.38
c = 89.813	γ = 90

Symmetry
Space Group	C 1 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	100	CCD	BRUKER PROTEUM-R	MONTEL OPTICS	2006-05-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	1.85	70.481	99.4	0.0353	23.9	14.3		83235

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)
	1.85	1.9	100		0.3115	3.19	5.09	6377

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	1Z90	1.85	70.481	83222	4158	99.371	0.195	0.192	0.22	0.239	0.25	RANDOM	11.405

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]
-0.363		-0.235	-0.398		0.676

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.005
r_dihedral_angle_3_deg	14.536
r_dihedral_angle_4_deg	13.597
r_dihedral_angle_1_deg	5.963
r_scangle_it	3.454
r_scbond_it	2.253
r_angle_refined_deg	1.902
r_mcangle_it	1.298
r_mcbond_it	0.868
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.005
r_dihedral_angle_3_deg	14.536
r_dihedral_angle_4_deg	13.597
r_dihedral_angle_1_deg	5.963
r_scangle_it	3.454
r_scbond_it	2.253
r_angle_refined_deg	1.902
r_mcangle_it	1.298
r_mcbond_it	0.868
r_nbtor_refined	0.308
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.134
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7132
Nucleic Acid Atoms
Solvent Atoms	871
Heterogen Atoms	62

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling

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.