Experiment: 9J7S

Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Providencia alcalifaciens complexed with Phe

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KFL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	16% PEG3350, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, and 2% v/v Tacsimate pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.234	α = 90
b = 51.468	β = 113.75
c = 132.657	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU HyPix-6000HE		2022-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.5	25.17	99.8	0.978	6.8	7.7		53799

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.58			0.736	1.6

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	1KFL	2.5	25.17	51076	2711	99.73	0.23583	0.23425	0.2417	0.2655	0.2732	RANDOM	33.025

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]
0.84		0.17	1.28		-1.63

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9280
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing