4M28 | pdb_00004m28

UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OEF	pdb entry 2OEF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	293.15	0.1 M MES, 20% w/v PEG-4000, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 6.4

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.25	α = 90
b = 108.47	β = 90
c = 152.59	γ = 90

Symmetry
Space Group	C 2 2 21

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	monochromator (horizontally side diffracting Silicon 111 crystal).	2013-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3	47.3	90	8	11.6	11	126117	11151	2	2	70

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	pdb entry 2OEF	3	47.27	11151	10539	546	90	0.21642	0.21642	0.21326	0.21	0.27914	0.28	RANDOM	84.193

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.569
r_dihedral_angle_3_deg	16.49
r_dihedral_angle_4_deg	13.663
r_long_range_B_refined	11.401
r_long_range_B_other	11.295
r_scangle_other	8.208
r_mcangle_it	7.58
r_mcangle_other	7.578
r_scbond_it	5.382
r_scbond_other	5.349
r_dihedral_angle_1_deg	5.203
r_mcbond_it	5.005
r_mcbond_other	5.005
r_angle_refined_deg	1.15
r_angle_other_deg	0.718
r_chiral_restr	0.056
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3730
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
MxCuBE	data collection
XDS	data reduction
SADABS	data scaling
CNS	phasing