6ZZP | pdb_00006zzp

Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psychrobacter arcticus complexed with NAD+ and 3-oxovalerate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZZO	D_1292104350

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.18 M succinic acid, 17.2% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.753	α = 90
b = 111.132	β = 90
c = 137.3	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	175	PIXEL	DECTRIS EIGER2 X 16M		2018-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.84	29.64	99.5	0.14	0.057	0.997	12	6.5		90721

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.88	89.88		0.943	0.406	0.738	2.1	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	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	D_1292104350	1.84	29.64	86146	4528	99.41	0.1479	0.1457	0.16	0.1893	0.2	RANDOM	20.873

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]
2.5			-1.15		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.381
r_dihedral_angle_4_deg	20.556
r_dihedral_angle_3_deg	13.435
r_dihedral_angle_1_deg	7.72
r_angle_other_deg	1.415
r_angle_refined_deg	1.412
r_chiral_restr	0.07
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.381
r_dihedral_angle_4_deg	20.556
r_dihedral_angle_3_deg	13.435
r_dihedral_angle_1_deg	7.72
r_angle_other_deg	1.415
r_angle_refined_deg	1.412
r_chiral_restr	0.07
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7500
Nucleic Acid Atoms
Solvent Atoms	1022
Heterogen Atoms	216

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.