8GEK | pdb_00008gek

Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LOY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystallization trials used the sitting drop vapour diffusion method, at 20 C, with droplets consisting of 150 nL of protein solution and 150 nL of reservoir solution. Rectangular CLsoDHDPS crystals were produced using the JCSG+ Suite screen in condition A2 (20% w/v polyethylene glycol 3000, 0.1 M sodium citrate, pH 5.5). For ligand bound structures, the crystals were soaked for 7 days in mother liquor with either: 100 mM lysine, 100 mM pyruvate or 100 mM of both succinic semi-aldehyde and pyruvate.

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.112	α = 90
b = 132.92	β = 99.79
c = 154.904	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	110	CCD	ADSC QUANTUM 315r		2018-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.93	45.81	99.5	0.082	0.998	7.8	3.94		151510

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	1.93	1.96			0.468

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.93	45.81	1.33	151353	4544	99.45	0.1864	0.1851	0.1862	0.2247	0.2258

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.884
f_angle_d	0.968
f_chiral_restr	0.241
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13476
Nucleic Acid Atoms
Solvent Atoms	969
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing