Experiment: 5IJQ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GSN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	Protein buffer: 3.5-5.0 mg/ml autotaxin in 50 mM Tris pH 8.0 and 150 mM NaCl Crystallization condition: 20% PEG 3350, 0.2 M ammonium iodide, 0.3 M sodium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.2	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.808	α = 98.78
b = 63.289	β = 106.22
c = 70.471	γ = 99.77

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	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.283	APS	23-ID-D

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	2.05	20	96.8	0.1	13.9	4.8		52153			30.2

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	2.05	2.12	93.9		0.38	2.49	3

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	2GSN	2.05	20	45374	2386	88.53	0.1562	0.154	0.16	0.1974	0.2	RANDOM	42.438

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]
0.83	-0.24	0.85	-0.08	-0.27	-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	37.045
r_sphericity_free	33.959
r_dihedral_angle_2_deg	33.349
r_dihedral_angle_4_deg	15.746
r_dihedral_angle_3_deg	11.711
r_dihedral_angle_1_deg	6.171
r_mcangle_it	3.68
r_mcbond_it	2.562
r_mcbond_other	2.542
r_angle_refined_deg	1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	37.045
r_sphericity_free	33.959
r_dihedral_angle_2_deg	33.349
r_dihedral_angle_4_deg	15.746
r_dihedral_angle_3_deg	11.711
r_dihedral_angle_1_deg	6.171
r_mcangle_it	3.68
r_mcbond_it	2.562
r_mcbond_other	2.542
r_angle_refined_deg	1.36
r_angle_other_deg	0.941
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6329
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	121

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
DENZO	data reduction

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.