5TX7

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Desulfovibrio vulgaris

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	0.2 ul of 19 mg/ml protein in 50 mM Tris pH 7.5, 300 mM NaCl, and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG II condition #21 (1M Ammonium Sulfate, 0.1M Bis-Tris, 1%w/v PEG 3350 pH=5.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.109	α = 90
b = 117.107	β = 90
c = 135.84	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315r		2014-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97912	APS	19-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	2.5	50.01	99.9	0.091	0.091	8.5	5.2		25228		-3	57.1

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	2.5	2.54	100		0.77	0.666	2.53	5.2	1269

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	2CUK	2.51	50	23947	1240	99.69	0.1768	0.1739	0.2298	RANDOM	68.79

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]
0.74			1.35		-2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.794
r_dihedral_angle_4_deg	16.675
r_dihedral_angle_3_deg	12.738
r_dihedral_angle_1_deg	6.109
r_mcangle_it	2.766
r_mcbond_it	1.747
r_mcbond_other	1.747
r_angle_refined_deg	1.362
r_angle_other_deg	0.944
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.794
r_dihedral_angle_4_deg	16.675
r_dihedral_angle_3_deg	12.738
r_dihedral_angle_1_deg	6.109
r_mcangle_it	2.766
r_mcbond_it	1.747
r_mcbond_other	1.747
r_angle_refined_deg	1.362
r_angle_other_deg	0.944
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4743
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	24

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

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 R01GM133198.