Experiment: 4V15

Crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GWQ	PDB ENTRY 3GWQ AND 3LLX
experimental model	PDB	3LLX	PDB ENTRY 3GWQ AND 3LLX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.1		13% (W/V) PEG-3350, 200 MM SODIUM CHLORIDE, 100 MM TRIS/HCL, PH 8.1

Crystal Properties
Matthews coefficient	Solvent content
2.2	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.267	α = 90
b = 84.278	β = 111.9
c = 72.852	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	CCD	MARMOSAIC 225 mm CCD	TOROIDAL FOCUSING	2008-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA		SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	47.65	99.6	0.08	6.3	7.4		111114		-3	12.65

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	1.5	1.55	100		0.33	1.6	7.4

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 3GWQ AND 3LLX	1.5	35.759	1.44	111114	5551	99.62	0.1499	0.1484	0.1491	0.1767	0.1769	19.5

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	14.626
f_angle_d	1.356
f_chiral_restr	0.057
f_bond_d	0.019
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5489
Nucleic Acid Atoms
Solvent Atoms	955
Heterogen Atoms	66

Software

Software
Software Name	Purpose
AUTOMAR	data reduction
SCALEPACK	data scaling
PHASER	phasing
Rosetta	phasing
PHENIX	refinement