5MH6

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	290	Protein buffer: 20 mM Tris-HCl pH8, 3 mM EDTA and 1 M NaCl Crystallisation conditions: 0.1M Tris-HCl pH8, 0.5 M magnesium acetate and 20 % PEG3350 Ligands: 5 mM NAD+ and 50 mM 2-ketohexanoic acid

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.455	α = 109.11
b = 75.008	β = 107.55
c = 77.555	γ = 95.91

Symmetry
Space Group	P 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 315		2008-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97204	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.35	46.54	93	0.061	23.6	2.1		268611

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37	91.7		0.462	2.1	2.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.35	46.54	219914	11807	80.19	0.12817	0.1264	0.16174	RANDOM	17.066

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	-0.1	-0.1	0.18	0.07	-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.952
r_sphericity_free	27.887
r_sphericity_bonded	21.444
r_dihedral_angle_4_deg	17.315
r_rigid_bond_restr	14.562
r_dihedral_angle_3_deg	10.546
r_scbond_other	6.955
r_scbond_it	6.946
r_dihedral_angle_1_deg	5.89
r_scangle_other	5.792
r_long_range_B_refined	5.655
r_long_range_B_other	5.161
r_mcangle_other	3.065
r_mcangle_it	3.064
r_mcbond_other	2.825
r_mcbond_it	2.824
r_angle_refined_deg	1.502
r_angle_other_deg	1.423
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9360
Nucleic Acid Atoms
Solvent Atoms	1738
Heterogen Atoms	346

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing