Experiment: 4V3F

Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with betaine aldehyde

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A0M	PDB ENTRY 4A0M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.2		AMMONIUM IODIDE 0.2 M, POLY ETHYLENE GLYCOL 3350 20% (W/V), PH 6.2

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.44	α = 79.44
b = 82.256	β = 84.89
c = 88.516	γ = 77.32

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	CCD	ADSC QUANTUM 210r		2014-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	29	96.1	0.048	0.048	9.1	2.4		122131		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	88		0.268	2.3	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PDB ENTRY 4A0M	1.998	28.968	1.96	122084	5965	96.04	0.1968	0.1961	0.1986	0.2114	0.2126

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	14.725
f_angle_d	1.259
f_chiral_restr	0.054
f_bond_d	0.009
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15246
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	90

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing