1Z90 | pdb_00001z90

X-ray structure of gene product from arabidopsis thaliana at3g03250, a putative UDP-glucose pyrophosphorylase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	293	1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K
2		5.5	293	1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.68	α = 90
b = 58.863	β = 100.4
c = 89.862	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	MARMOSAIC 225 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-03-13	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM		APS	22-BM
2	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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
1,2	1.863	37.365	98	0.066	17.377	7		79505

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)
	1.86	1.9	89.5		0.395	3.224	5.1

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	SAD	THROUGHOUT	1.86	50	75518	3986	97.7	0.20319	0.201	0.2	0.249	0.25	RANDOM	31.48

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]
-0.79		-1.22	-0.25		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.434
r_dihedral_angle_4_deg	17.45
r_dihedral_angle_3_deg	16.783
r_angle_other_deg	16.409
r_scangle_it	6.843
r_dihedral_angle_1_deg	6.359
r_scbond_it	4.837
r_mcangle_it	2.948
r_mcbond_it	1.73
r_angle_refined_deg	1.607
r_mcbond_other	0.411
r_nbtor_refined	0.312
r_nbtor_other	0.288
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.214
r_symmetry_vdw_refined	0.198
r_nbd_other	0.168
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.11
r_bond_other_d	0.097
r_gen_planes_other	0.033
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7122
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
RESOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing