5UPR | pdb_00005upr

X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2 M Ammonium Sulphate, 0.1 M Bis-Tris, 25 % PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.368	α = 90
b = 115.533	β = 90.02
c = 78.719	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	CCD	MARMOSAIC 300 mm CCD	beryllium lenses	2016-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97875	APS	21-ID-G

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	30	99.9	0.1	15.04	3.9		67710

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	2	2.03	100		0.65	2.86	3.9	3393

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	2	30	63148	3412	97.87	0.16784	0.16575	0.18	0.20794	0.21	RANDOM	30.016

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]
0.18		-0.08	-0.54		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.005
r_dihedral_angle_4_deg	17.017
r_dihedral_angle_3_deg	13.72
r_dihedral_angle_1_deg	6.242
r_long_range_B_refined	5.718
r_long_range_B_other	5.463
r_scangle_other	2.583
r_angle_refined_deg	1.812
r_mcangle_it	1.754
r_mcangle_other	1.754
r_scbond_it	1.682
r_scbond_other	1.643
r_mcbond_it	1.144
r_mcbond_other	1.143
r_angle_other_deg	1.011
r_chiral_restr	0.104
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	7778
Nucleic Acid Atoms
Solvent Atoms	1023
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	phasing
Coot	model building