5BW6 | pdb_00005bw6

Tryptophan Synthase from Salmonella typhimurium in complex with a single molecule of 2-({[4-(trifluoromethoxy)phenyl]carbonyl}amino)ethyl dihydrogen phosphate (F6) in the alpha-site.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WX2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	50mM Bicine-NaOH, pH 7.8, containing 50mM NaCl, 2mM spermine, and 10% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.03	α = 90
b = 58.9	β = 94.91
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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax	2013-03-01	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)	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	1.82	20	72.8	0.043	0.043	0.056	0.035	0.999	13.1	2.1	46573	46573

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	1.82	1.92	69.7		0.454	0.018	0.014	0.756	2	2.1	6445

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	4WX2	1.82	19.83	44334	2237	72.58	0.1705	0.1682	0.17	0.2143	0.21	RANDOM	25.879

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]
-0.04		-0.03	0.05		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.417
r_dihedral_angle_4_deg	18.657
r_dihedral_angle_3_deg	14.47
r_dihedral_angle_1_deg	6.187
r_angle_refined_deg	1.655
r_mcangle_it	1.238
r_scbond_it	0.875
r_mcbond_it	0.705
r_chiral_restr	0.108
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.417
r_dihedral_angle_4_deg	18.657
r_dihedral_angle_3_deg	14.47
r_dihedral_angle_1_deg	6.187
r_angle_refined_deg	1.655
r_mcangle_it	1.238
r_scbond_it	0.875
r_mcbond_it	0.705
r_chiral_restr	0.108
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4924
Nucleic Acid Atoms
Solvent Atoms	673
Heterogen Atoms	37

Software

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

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.