9TME | pdb_00009tme

Structure of Plasmodium falciparum Transketolase in complex with Oxythiamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8R3Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.2M potassium citrate diabasic monohydrate, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.388	α = 90
b = 142.81	β = 90
c = 176.185	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS EIGER2 XE 16M		2025-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.81	110.942	99.19	0.995	7.1	13.7		260015

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.813	1.884			0.395

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.813	110.942	258211	12987	99.191	0.183	0.1809	0.1931	0.217	0.2274	21.444

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]
-1.393			1.883		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.21
r_dihedral_angle_4_deg	16.715
r_dihedral_angle_3_deg	14.317
r_dihedral_angle_1_deg	6.898
r_lrange_it	4.986
r_lrange_other	4.986
r_scangle_it	3.842
r_scangle_other	3.842
r_scbond_it	2.461
r_scbond_other	2.461
r_mcangle_it	2.002
r_mcangle_other	2.002
r_angle_refined_deg	1.516
r_mcbond_it	1.419
r_mcbond_other	1.419
r_angle_other_deg	1.399
r_symmetry_xyhbond_nbd_other	0.219
r_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.198
r_nbd_other	0.178
r_symmetry_nbd_other	0.175
r_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.169
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21136
Nucleic Acid Atoms
Solvent Atoms	1981
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
REFMAC	phasing