3O9Z

Crystal structure of the WlbA (WbpB) dehydrogenase from Thermus thermophilus in complex with NAD and alpha-ketoglutarate at 1.45 angstrom resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	15-20% PEG-5000, 100 mM MOPS, 20 mM alpha-ketoglutarate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.781	α = 90
b = 68.199	β = 94.66
c = 164.053	γ = 90

Symmetry
Space Group	P 1 21 1

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 210r	mirrors	2009-11-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97918,0.97953,0.97150	APS	19-BM

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	1.449	50	96.8	0.061	0.061	44.4	3.6	270515	270515

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.449	1.48	88.7		0.167	0.167	4.2	2.3	12317

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.449	30	270490	270490	13628	96.7	0.1953	0.1953	0.19367	0.22649	RANDOM	25.016

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]
1.7		0.3	-0.58		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.505
r_dihedral_angle_4_deg	20.726
r_dihedral_angle_3_deg	15.225
r_dihedral_angle_1_deg	7.308
r_scangle_it	5.751
r_scbond_it	3.725
r_mcangle_it	2.524
r_angle_refined_deg	2.348
r_mcbond_it	1.772
r_chiral_restr	0.141
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9799
Nucleic Acid Atoms
Solvent Atoms	1216
Heterogen Atoms	232

Software

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