2R5N | pdb_00002r5n

Crystal structure of transketolase from Escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QGD	PDB entry 1QGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	281	50 mM glycyl-glycine, 10 mM thiamin diphosphate, 5 mM calcium chloride, 19-22% PEG6000, 1% glycerol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.969	α = 90
b = 101.738	β = 90
c = 132.859	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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2007-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	35	94.7	0.111	0.111	4.9	12.1	184035	184180	3	3	23.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	68.7		0.988	0.988	0.8	5.3	19193

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 1QGD	1.6	35	160722	159774	8028	99.41	0.169	0.164	0.163	0.16	0.196	0.19	RANDOM	12.34

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]
-0.41			0.06		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.578
r_dihedral_angle_4_deg	16.461
r_dihedral_angle_3_deg	11.503
r_dihedral_angle_1_deg	5.623
r_scangle_it	2.533
r_scbond_it	1.634
r_angle_refined_deg	1.23
r_mcangle_it	0.867
r_mcbond_it	0.506
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.578
r_dihedral_angle_4_deg	16.461
r_dihedral_angle_3_deg	11.503
r_dihedral_angle_1_deg	5.623
r_scangle_it	2.533
r_scbond_it	1.634
r_angle_refined_deg	1.23
r_mcangle_it	0.867
r_mcbond_it	0.506
r_nbtor_refined	0.305
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.167
r_metal_ion_refined	0.135
r_xyhbond_nbd_refined	0.109
r_symmetry_hbond_refined	0.097
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10198
Nucleic Acid Atoms
Solvent Atoms	1628
Heterogen Atoms	160

Software

Software
Software Name	Purpose
d*TREK	data scaling
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.