9IBE | pdb_00009ibe

D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with potassium, 2-ketohexanoic acid, NADP+ and chloride

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QZB	search with dimer of domain 2 (find 2 copies) and single domain 1 (find 4 copies)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	290	protein buffer: 20 mM Tris/HCl pH 8.0 2 mM EDTA 1 M KCl 50 mM 2-ketohexanoic acid 5 mM NAD+ Well Solution: 0.1 M Mg acetate 26 % PEG 3350 0.1 M Tris/HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.633	α = 108.841
b = 75.34	β = 108.084
c = 78.234	γ = 95.526

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 X 16M		2023-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.940535	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	1.26	52.3	92.2	0.059	0.99	12	3.8		332819			11.7

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	1.26	1.28	89.4		0.99	0.33	0.8	3.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.26	52.276	332807	16700	92.234	0.154	0.1518	0.1598	0.1876	0.1924	Random	18.037

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]
0.33	-0.178	-0.216	0.191	0.214	-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.692
r_lrange_other	16.816
r_dihedral_angle_6_deg	16.326
r_scangle_it	15.12
r_scangle_other	15.119
r_dihedral_angle_2_deg	13.176
r_scbond_it	11.646
r_scbond_other	11.646
r_dihedral_angle_3_deg	10.379
r_mcangle_other	10.013
r_mcangle_it	10.012
r_mcbond_it	7.814
r_mcbond_other	7.811
r_dihedral_angle_1_deg	6.681
r_rigid_bond_restr	4.08
r_dihedral_angle_other_2_deg	3.434
r_angle_refined_deg	1.837
r_angle_other_deg	0.784
r_symmetry_nbd_refined	0.268
r_nbd_refined	0.248
r_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.186
r_symmetry_nbd_other	0.168
r_nbtor_refined	0.168
r_metal_ion_refined	0.131
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.072
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
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	1569
Heterogen Atoms	268

Software

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