8SKF | pdb_00008skf

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Lattice Translocation Disorder)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7SWK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	JCSG+ C4: 10% (w/v) PEG 6K, 0.10 M HEPES pH 7.0, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Plate: 13125, well C4 drop 2. Puck: PSL-0714, Cryo: 20% PEG200 + 80% crystallant. 2mM NAD added prior to crystallization. The intensities were corrected for lattice translocation disorder which orginally caused high Rfactors (~25% and 29% for R and Rfree) and residual positive electron density throughout the polypeptide chains. The correction was based on major non-origin Patterson peaks, 1) (0.500, 0.027, 0.500) and its inverse (0.500, -0.027, 0.500) and 2) (0.000, 0.054, 0.000)

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.822	α = 90
b = 184.823	β = 90
c = 163.066	γ = 90

Symmetry
Space Group	C 2 2 21

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 9M		2022-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9795	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.8	163.07	100	0.155	0.161	0.043	0.999	10.5	13.7		119740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85		99.9	1.439	1.495	0.404	0.886		13.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	81.53	1.33	119370	5962	99.69	0.1758	0.1741	0.18	0.2074	0.21

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.458
f_angle_d	0.99
f_chiral_restr	0.056
f_bond_d	0.01
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7492
Nucleic Acid Atoms
Solvent Atoms	813
Heterogen Atoms	152

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
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.