5XQK

Crystal Structure of Transketolase in complex with xylulose-5-phosphate from Pichia Stipitis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HYV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1M MES, 0.1M NaCl, PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.709	α = 90
b = 183.724	β = 90
c = 98.856	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	RAYONIX MX300HE		2015-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1	NSRRC	BL15A1

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	1.12	30	99.6	0.04	30.2	7.8		312132

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	1.12	1.14	99.9		0.602	2.9	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5HYV	1.12	30	312132	16024	94.29	0.12305	0.12252	0.13352	RANDOM	17.951

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]
0.31			-0.15		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.945
r_sphericity_free	25.218
r_dihedral_angle_4_deg	16.582
r_dihedral_angle_3_deg	11.347
r_sphericity_bonded	6.015
r_dihedral_angle_1_deg	5.977
r_long_range_B_refined	2.544
r_rigid_bond_restr	2.37
r_long_range_B_other	2.076
r_scangle_other	1.56
r_angle_refined_deg	1.451
r_scbond_it	1.318
r_scbond_other	1.317
r_mcangle_it	1.128
r_mcangle_other	1.128
r_angle_other_deg	1.059
r_mcbond_it	0.872
r_mcbond_other	0.871
r_chiral_restr	0.084
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5130
Nucleic Acid Atoms
Solvent Atoms	756
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data reduction
HKL-2000	data scaling