6DZ4 | pdb_00006dz4

Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HN4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	297	50mM Bicine-NaOH, pH 7.8, containing 9% PEG3350, 50mM NaCl, 2mM spermine

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.509	α = 90
b = 59.3	β = 94.69
c = 67.325	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 315		2015-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	0.97930	ALS	12.3.1

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)	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	1.45	30	99.5	0.085	0.085	0.094	0.039	0.998	9.9	5.6	126505	126505

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)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	98.1		0.632	0.041	0.045	0.018	0.859		5.3

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	4HN4	1.45	28.94	120118	6241	99.46	0.1488	0.1469	0.15	0.1856	0.19	RANDOM	23.82

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]
-0.41		0.05	0.11		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.401
r_sphericity_free	27.023
r_dihedral_angle_4_deg	18.262
r_sphericity_bonded	13.018
r_dihedral_angle_3_deg	11.997
r_dihedral_angle_1_deg	6.052
r_rigid_bond_restr	1.788
r_angle_refined_deg	1.376
r_chiral_restr	0.091
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.401
r_sphericity_free	27.023
r_dihedral_angle_4_deg	18.262
r_sphericity_bonded	13.018
r_dihedral_angle_3_deg	11.997
r_dihedral_angle_1_deg	6.052
r_rigid_bond_restr	1.788
r_angle_refined_deg	1.376
r_chiral_restr	0.091
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4922
Nucleic Acid Atoms
Solvent Atoms	767
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.