6VVI

Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1)

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
2.91	57.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.468	α = 90
b = 98.1	β = 90
c = 176.866	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	2.14	49.1	99.4	0.999	11.5	6.7		90994

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	2.14	2.2			0.865

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	THROUGHOUT	4DPP	2.145	49.098	90925	4371	99.238	0.173	0.1715	0.2091	40.455

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]
-1.039			3.471		-2.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.487
r_dihedral_angle_4_deg	15.759
r_dihedral_angle_3_deg	14.108
r_dihedral_angle_1_deg	6.926
r_lrange_it	6.321
r_lrange_other	6.317
r_scangle_other	5.025
r_scangle_it	5.023
r_mcangle_other	3.277
r_mcangle_it	3.276
r_scbond_it	3.198
r_scbond_other	3.198
r_mcbond_it	2.299
r_mcbond_other	2.292
r_angle_refined_deg	1.404
r_angle_other_deg	1.287
r_nbd_refined	0.193
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.163
r_nbtor_refined	0.153
r_nbd_other	0.129
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.068
r_symmetry_nbd_refined	0.02
r_metal_ion_refined	0.013
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9633
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	53

Software

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