6O1H | pdb_00006o1h

Tryptophan synthase Q114A mutant in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	100 mM Bicine-CsOH, pH 7.8, 5-10% PEG8000, 2 mM F9F, 0.01 mM PLP

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.749	α = 90
b = 60.72	β = 94.63
c = 67.21	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 Confocal Max-Flux	2018-10-02	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	1.64	40	99.9	0.051	0.051	0.06	0.031	0.999	11.5	3.5		90369			16.7

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	1.64	1.73	99.5		0.306	0.306	0.364	0.195	2.4	3.4

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	PDB entry 4HPJ	1.64	39.31	85508	4448	99.42	0.156	0.1538	0.15	0.199	0.2	RANDOM	29.599

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]
0.88		0.14	-0.81		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.805
r_dihedral_angle_4_deg	15.609
r_dihedral_angle_3_deg	12.593
r_rigid_bond_restr	7.957
r_dihedral_angle_1_deg	6.309
r_angle_refined_deg	1.24
r_chiral_restr	0.094
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4950
Nucleic Acid Atoms
Solvent Atoms	743
Heterogen Atoms	119

Software

Software
Software Name	Purpose
CrystalClear	data collection
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
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.