6UE0

Crystal structure of dihydrodipicolinate synthase from Klebsiella pneumoniae bound to pyruvate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris, ph 7.5, 2 M Ammonium Sulfate, 5 mM Pyruvate

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.634	α = 90
b = 114.23	β = 90
c = 55.298	γ = 90

Symmetry
Space Group	P 21 21 2

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	DECTRIS EIGER X 16M		2018-03-08	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)	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	1.89	49.039	99.7	0.998	11.4	6.7		54112

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	1.89	1.93	95.3		0.827

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1YXC	1.892	48.99	54037	2562	99.666	0.171	0.1693	0.1982	22.372

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]
-0.034			-0.847		0.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.125
r_dihedral_angle_4_deg	15.829
r_dihedral_angle_3_deg	13.191
r_dihedral_angle_1_deg	6.666
r_lrange_it	4.525
r_lrange_other	4.393
r_scangle_it	3.522
r_scangle_other	3.488
r_scbond_it	2.203
r_scbond_other	2.179
r_mcangle_other	1.947
r_mcangle_it	1.944
r_angle_refined_deg	1.398
r_angle_other_deg	1.359
r_mcbond_it	1.32
r_mcbond_other	1.308
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.185
r_symmetry_nbd_other	0.168
r_nbd_other	0.152
r_nbtor_refined	0.149
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.098
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4370
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing