3MOS | pdb_00003mos

The structure of human Transketolase

X-RAY DIFFRACTION

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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	298	Crystallization trials revealed a reservoir mixture of 13.5-15 % PEG 6000 (w/v), 4% PEG 400 (v/v) and 2% glycerol (v/v) in 50 mM glycyl-glycine (pH 7.9) optimal for reproducible crystallization of single crystals. To induce crystallization 3 l protein solution (8-12 mg/ml, 0.6 mM ThDP, 5 mM CaCl2 in 50 mM glycyl-glycine (pH 7.9)) were mixed with 3 l of the reservoir solution at room temperature. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.63	α = 90
b = 85.33	β = 125.69
c = 72.74	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	93	IMAGE PLATE	RIGAKU RAXIS IV++	Varimax HR	2008-05-26	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	1.75	20	98	0.05	0.063	14.78	2.5	57086	55932	2.8	-3	27.5

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)
	1.75	1.85	96.2		0.394	0.494	2.8	2.4	8724

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	1.75	20	55932	55928	2796	98.41	0.164	0.164	0.162	0.16	0.206	0.16	RANDOM	21.521

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]
-0.77		0.36	0.48		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.287
r_dihedral_angle_4_deg	18.51
r_dihedral_angle_3_deg	14.264
r_dihedral_angle_1_deg	6.5
r_scangle_it	4.686
r_scbond_it	2.998
r_angle_refined_deg	1.995
r_mcangle_it	1.819
r_mcbond_it	1.182
r_chiral_restr	0.146
r_bond_refined_d	0.024
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4715
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	68

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction