9LL3 | pdb_00009ll3

X-ray structure of Enterobacter cloaca transaldolase in complex with D-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	3S1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	100 mM cacodylate buffer, pH 6.5, 10% (w/v) PEG3000, 10% (w/v) PEG 8000, 200 mM of MgCl2, 20 mM dihydroxtacetone, 20 mM, 20 mM D,L-glyceraldehyde-3-phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.56	α = 90
b = 179.96	β = 90
c = 133.58	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	IMAGE PLATE	RIGAKU RAXIS VII		2019-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.92	19.6	99.8	0.117	0.998	14.7	7.2		90439

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.97			0.912	0.771	2.3	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3S1V	1.92	19.6	85902	4537	99.84	0.16762	0.16583	0.1776	0.20128	0.2114	RANDOM	20.293

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]
0.02			0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.61
r_dihedral_angle_2_deg	11.557
r_dihedral_angle_1_deg	6.652
r_long_range_B_refined	6.282
r_long_range_B_other	6.254
r_scangle_other	5.039
r_scbond_it	3.4
r_scbond_other	3.387
r_mcangle_other	2.273
r_mcangle_it	2.272
r_mcbond_it	1.661
r_mcbond_other	1.659
r_angle_refined_deg	1.119
r_angle_other_deg	0.435
r_chiral_restr	0.06
r_gen_planes_refined	0.01
r_bond_refined_d	0.004
r_gen_planes_other	0.001
r_bond_other_d
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8170
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing