8QZA | pdb_00008qza

D-2-hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterranei apo-enzyme (2.25 A resolution)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MH5

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 Crystallization condition: 0.1 M TRIS/HCl pH 8.0 0.5 M Magnesium acetate 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.352	α = 90
b = 75.986	β = 93.991
c = 74.589	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	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	2.25	29.45	98.8	0.041	0.99	11.9	6.8		32656

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	2.25	2.33	88		0.42	0.79		5.1

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	2.252	29.45	32639	1645	98.774	0.193	0.1899	0.197	0.2512	0.2497	65.302

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]
-1.65		1.126	2.006		-0.508

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.339
r_dihedral_angle_6_deg	16.237
r_lrange_other	13.885
r_lrange_it	13.869
r_dihedral_angle_2_deg	11.921
r_scangle_it	11.161
r_scangle_other	11.16
r_mcangle_it	10.67
r_mcangle_other	10.669
r_dihedral_angle_1_deg	8.219
r_scbond_it	7.645
r_scbond_other	7.644
r_mcbond_it	7.374
r_mcbond_other	7.374
r_angle_refined_deg	1.939
r_angle_other_deg	0.744
r_nbd_refined	0.211
r_nbd_other	0.169
r_symmetry_nbd_other	0.168
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.164
r_ncsr_local_group_1	0.132
r_metal_ion_refined	0.119
r_symmetry_nbd_refined	0.11
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4698
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing