8TG2 | pdb_00008tg2

The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with products UDP-Glucose and PPi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	200 mM ammonium acetate, 100 mM tri-sodium citrate, pH 5.4 - 5.6, and 15% - 17% polyethylene glycol-4000 (PEG-4000)

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.09	α = 90
b = 121.9	β = 105.69
c = 60.96	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	PIXEL	DECTRIS PILATUS 6M		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	2.4	52.6	100	0.0451	0.027	0.999	19	6.92		29455			76.042

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.5	99.9		0.5176	0.402	0.901		6.67

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	52.59	27910	1544	99.97	0.20784	0.2063	0.2105	0.23626	0.2384	RANDOM	71.313

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]
-0.58		-1.68	-1.02		2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.587
r_dihedral_angle_4_deg	16.829
r_dihedral_angle_3_deg	15.916
r_long_range_B_refined	9.368
r_long_range_B_other	9.363
r_mcangle_it	7.09
r_mcangle_other	7.089
r_scangle_other	7.006
r_dihedral_angle_1_deg	5.386
r_scbond_it	5.166
r_scbond_other	5.112
r_mcbond_other	5.096
r_mcbond_it	5.095
r_angle_other_deg	2.225
r_angle_refined_deg	1.238
r_chiral_restr	0.059
r_bond_other_d	0.035
r_gen_planes_other	0.024
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4706
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing