4ZQC | pdb_00004zqc

Tryptophan Synthase from Salmonella typhimurium in complex with two molecules of N-(4'-trifluoromethoxybenzoyl)-2-amino-1-ethylphosphate (F6F) inhibitor in the alpha-site and a single F6F molecule in the beta-site at 1.54 Angstrom resolution.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Y6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	50 mM Bicine-NaOH, containing 10-14% PEG 8,000, and 2 mM spermine

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.529	α = 90
b = 58.63	β = 94.92
c = 67.22	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		2015-04-18	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	1.54	30	95	0.105	0.105	0.123	0.063	0.987	7.2	3.8	99870	99870

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.62	92.4		0.556	0.044	0.026	0.813	2.1	3.8	14139

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	4Y6G	1.54	29.31	94912	4955	94.77	0.1382	0.1357	0.1351	0.1866	0.1865	RANDOM	20.132

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]
0.19		-0.05	-0.33		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.105
r_dihedral_angle_2_deg	36.569
r_sphericity_bonded	19.13
r_dihedral_angle_4_deg	17.931
r_dihedral_angle_3_deg	12.066
r_dihedral_angle_1_deg	5.778
r_scbond_it	2.608
r_mcangle_it	2.456
r_rigid_bond_restr	2.371
r_mcbond_it	1.863

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.105
r_dihedral_angle_2_deg	36.569
r_sphericity_bonded	19.13
r_dihedral_angle_4_deg	17.931
r_dihedral_angle_3_deg	12.066
r_dihedral_angle_1_deg	5.778
r_scbond_it	2.608
r_mcangle_it	2.456
r_rigid_bond_restr	2.371
r_mcbond_it	1.863
r_angle_refined_deg	1.736
r_chiral_restr	0.114
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5018
Nucleic Acid Atoms
Solvent Atoms	869
Heterogen Atoms	127

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
SCALA	data scaling
MOLREP	phasing
DM	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

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.