3FLK

Crystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH, oxalate and metal ion

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.75 M ammonium sulfate, 0.2 M potassium acetate, 0.02 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.278	α = 90
b = 117.278	β = 90
c = 291.324	γ = 90

Symmetry
Space Group	P 43 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	IMAGE PLATE	MAR scanner 300 mm plate		2008-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9794	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	109.11	99	0.112	21.4	12.2		126431

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	90		0.307	4.97	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2	50	126431	6868	99.02	0.20862	0.20764	0.22692	RANDOM	21.388

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]
0.19			0.19		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.824
r_dihedral_angle_4_deg	15.48
r_dihedral_angle_3_deg	13.481
r_dihedral_angle_1_deg	5.124
r_scangle_it	1.498
r_angle_refined_deg	1.025
r_scbond_it	0.971
r_mcangle_it	0.681
r_mcbond_it	0.459
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.824
r_dihedral_angle_4_deg	15.48
r_dihedral_angle_3_deg	13.481
r_dihedral_angle_1_deg	5.124
r_scangle_it	1.498
r_angle_refined_deg	1.025
r_scbond_it	0.971
r_mcangle_it	0.681
r_mcbond_it	0.459
r_nbtor_refined	0.299
r_nbd_refined	0.178
r_symmetry_vdw_refined	0.123
r_xyhbond_nbd_refined	0.086
r_symmetry_hbond_refined	0.084
r_chiral_restr	0.076
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11248
Nucleic Acid Atoms
Solvent Atoms	919
Heterogen Atoms	302

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.