7KU9 | pdb_00007ku9

The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site, two molecules of F6F inhibitor at the enzyme alpha-site and another F6F molecule at the enzyme beta-site at 1.40 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HT3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.259	α = 90
b = 58.9	β = 94.82
c = 67.23	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	PIXEL	DECTRIS PILATUS 6M		2020-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9793	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.4	91.306	97.1	0.061	0.061	0.081	0.041	8.8	3.8	136186	136186

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	82.2		0.438	0.438	0.042	0.021	1.7	2.9

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	4HT3	1.4	36.79	129318	6868	97	0.138	0.136	0.14	0.177	0.18	RANDOM	20.67

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]
-0.06		0.07	-0.73		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.697
r_dihedral_angle_4_deg	19.168
r_dihedral_angle_3_deg	12.295
r_rigid_bond_restr	6.401
r_dihedral_angle_1_deg	6.041
r_angle_refined_deg	1.406
r_chiral_restr	0.099
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4930
Nucleic Acid Atoms
Solvent Atoms	892
Heterogen Atoms	239

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
MOLREP	phasing
DM	phasing
PDB_EXTRACT	data extraction