4S2C | pdb_00004s2c

Covalent complex of E. coli transaldolase TalB with fructose-6-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UCW	PDB ENTRY 1UCW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.2	0.2 M DL-malic acid, pH 7.0, 19% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.656	α = 90
b = 91.152	β = 90
c = 130.725	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	PIXEL	DECTRIS PILATUS 6M		2013-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.91914	Diamond	I02

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	2.2	29.43	99.5	0.094	12.7	4.8	41815	41815

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	2.2	2.26	97.6		0.491	3.7	4.5

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 (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 1UCW	2.2	29.43	39558	39703	2054	99.36	0.15586	0.1529	0.16	0.21103	0.21	RANDOM	30.733

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]
1.65			0.59		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.334
r_sphericity_free	33.349
r_dihedral_angle_4_deg	17.938
r_sphericity_bonded	14.847
r_dihedral_angle_3_deg	14.341
r_dihedral_angle_1_deg	5.428
r_scbond_it	5.158
r_mcangle_it	5.035
r_mcbond_it	4.126
r_mcbond_other	4.125
r_rigid_bond_restr	3.236
r_angle_refined_deg	1.311
r_angle_other_deg	0.806
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4944
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	34

Software

Software
Software Name	Purpose
ProDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling