7G6Z | pdb_00007g6z

Crystal Structure of rat Autotaxin in complex with 2-chloro-7-[(4-fluorophenyl)methyl]-9-methylpurin-8-one

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model		in house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.304	α = 90
b = 92.277	β = 90
c = 120.397	γ = 90

Symmetry
Space Group	P 21 21 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	PSI PILATUS 6M		2014-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.53	48.99	99.9	0.113	0.123	0.998	11.8	6.524		141669			28.303

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.57	99.8		2.403	2.617	0.396	0.94	6.457

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	inhouse model	1.53	48.99	121746	6425	90.42	0.2094	0.2078	0.2073	0.2402	0.2398	RANDOM	24.077

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]
-0.88			0.28		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.259
r_dihedral_angle_4_deg	15.347
r_dihedral_angle_3_deg	12.91
r_dihedral_angle_1_deg	6.408
r_mcangle_it	2.804
r_scbond_it	2.629
r_mcbond_it	1.826
r_angle_refined_deg	1.644
r_chiral_restr	0.118
r_bond_refined_d	0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.259
r_dihedral_angle_4_deg	15.347
r_dihedral_angle_3_deg	12.91
r_dihedral_angle_1_deg	6.408
r_mcangle_it	2.804
r_scbond_it	2.629
r_mcbond_it	1.826
r_angle_refined_deg	1.644
r_chiral_restr	0.118
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6500
Nucleic Acid Atoms
Solvent Atoms	594
Heterogen Atoms	123

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.