3M7I | pdb_00003m7i

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate(pyranose form) and magnesium 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	7.5		.2 M NaCl 30% Peg 400 0.1 M HEPES 10 mM RP5, 10 mM TPP, 1mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.337	α = 90
b = 70.955	β = 109.4
c = 69.189	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	1.75	40	97.5	0.094	12.7	3.2	59272	57827	2	2	34.3

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	1.75	1.78	99.9		0.415	3.2	2.9	2940

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3M34	1.75	40	2	2	57816	54908	2908	96.76	0.194	0.17121	0.16711	0.18	0.21076	0.22	RANDOM	23.719

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]
-0.54		0.96	1.03		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.646
r_dihedral_angle_4_deg	15.121
r_dihedral_angle_3_deg	13.709
r_dihedral_angle_1_deg	6.101
r_scangle_it	5.043
r_scbond_it	3.136
r_mcangle_it	1.893
r_angle_refined_deg	1.858
r_mcbond_it	1.11
r_angle_other_deg	1.024
r_mcbond_other	0.367
r_chiral_restr	0.114
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
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	328
Heterogen Atoms	45

Software

Software
Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing