5TEM

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,6 Pyridine Dicarboxylic and NADH

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.639	α = 90
b = 112.588	β = 90
c = 62.432	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	CCD	MARMOSAIC 300 mm CCD		2014-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.2	65.56	95.4	0.112	0.112	6.2	4.7		28190		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	95.7		0.493	0.851	2.1	4.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ARZ	2.2	65.56	26798	1368	95.22	0.1925	0.1908	0.2236	RANDOM	32.26

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]
1.3			-1.83		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.919
r_dihedral_angle_4_deg	19.388
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	5.879
r_angle_other_deg	3.831
r_mcangle_it	2.448
r_angle_refined_deg	1.716
r_mcbond_it	1.477
r_mcbond_other	1.476
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.919
r_dihedral_angle_4_deg	19.388
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	5.879
r_angle_other_deg	3.831
r_mcangle_it	2.448
r_angle_refined_deg	1.716
r_mcbond_it	1.477
r_mcbond_other	1.476
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_other	0.011
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3929
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.