3M6L

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M34

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	291	0.2 M NaCl, 20 % PEG 1000, 0.1 M Na/K phosphate, 10mM TPP, 10 mM R5P, 1mM CaCl2, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.924	α = 90
b = 71.462	β = 109.48
c = 69.617	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315r	mirrors	2010-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	1.59	40	94.8	0.085	19	3.8	80420	76588	1.9	2	27

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	1.59	1.63	72.1		0.74	1.9	3.4	2898

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3M34	1.59	40	1.9	76498	72677	3821	94.28	0.18	0.16173	0.15968	0.20086	RANDOM	15.947

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]
-0.52		1.83	1.06		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.2
r_dihedral_angle_4_deg	14.355
r_dihedral_angle_3_deg	14.111
r_dihedral_angle_1_deg	6.065
r_scangle_it	5.794
r_scbond_it	3.709
r_mcangle_it	2.241
r_angle_refined_deg	2.17
r_mcbond_it	1.404
r_angle_other_deg	1.122
r_mcbond_other	0.486
r_chiral_restr	0.14
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4901
Nucleic Acid Atoms
Solvent Atoms	565
Heterogen Atoms	56

Software

Software
Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling