8QZB | pdb_00008qzb

D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid, NAD+ and chloride (1.16 A resolution)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MH6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	290	Protein buffer: 20mM Tris/HCl pH 8.0 2mM EDTA 1M NaCl 50mM 2-ketohexanoic acid 5mM NAD+ Crystallisation conditions: 0.1M Tris/HCl pH 8.0 0.5M Magnesium acetate 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.182	α = 109.074
b = 74.777	β = 107.882
c = 78.172	γ = 95.56

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	PIXEL	DECTRIS EIGER2 XE 16M		2023-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9801	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	1.16	46.633	93.9	0.042	0.94	17.1	3.6		427918

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.16	1.18	83.7		0.5	0.56		3.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.16	46.633	427883	21342	93.897	0.136	0.1346	0.133	0.1651	0.1636	14.538

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]
0.041	-0.179	-0.092	0.243	0.081	-0.159

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	20.022
r_lrange_other	18.124
r_dihedral_angle_6_deg	17.509
r_scangle_it	14.943
r_scangle_other	14.942
r_dihedral_angle_3_deg	12.192
r_scbond_it	11.645
r_scbond_other	11.644
r_mcangle_it	11.423
r_mcangle_other	11.422
r_dihedral_angle_2_deg	11.294
r_mcbond_it	9.115
r_mcbond_other	9.111
r_dihedral_angle_1_deg	6.448
r_rigid_bond_restr	4.983
r_angle_refined_deg	1.689
r_angle_other_deg	0.706
r_symmetry_nbd_refined	0.277
r_symmetry_xyhbond_nbd_refined	0.236
r_nbd_refined	0.228
r_nbd_other	0.203
r_metal_ion_refined	0.198
r_nbtor_refined	0.174
r_symmetry_nbd_other	0.172
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.073
r_dihedral_angle_other_2_deg	0.065
r_symmetry_xyhbond_nbd_other	0.052
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_xyhbond_nbd_other	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9396
Nucleic Acid Atoms
Solvent Atoms	1619
Heterogen Atoms	266

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing