6VVH

Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) in complex with lysine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES (pH 7.5), 0.1 M NaCl, and 1.4 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.044	α = 90
b = 97.626	β = 90
c = 176.543	γ = 90

Symmetry
Space Group	P 21 21 21

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		2017-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9536	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	1.79	45.931	99.6	0.999	11.6	6.8		153659

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	1.79	1.84			0.857

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	4DPP	1.792	45.93	153294	7721	99.403	0.167	0.1656	0.196	26.23

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]
-0.862			1.86		-0.997

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.79
r_dihedral_angle_4_deg	16.764
r_dihedral_angle_3_deg	12.969
r_dihedral_angle_1_deg	6.657
r_lrange_it	5.033
r_lrange_other	5.033
r_scangle_it	3.619
r_scangle_other	3.619
r_scbond_it	2.316
r_scbond_other	2.316
r_mcangle_it	2.144
r_mcangle_other	2.144
r_mcbond_it	1.488
r_mcbond_other	1.488
r_angle_refined_deg	1.385
r_angle_other_deg	1.339
r_symmetry_nbd_refined	0.299
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.182
r_symmetry_nbd_other	0.173
r_nbd_other	0.171
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.155
r_symmetry_xyhbond_nbd_other	0.135
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.073
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	9661
Nucleic Acid Atoms
Solvent Atoms	1010
Heterogen Atoms	77

Software

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