7Z3K | pdb_00007z3k

Autotaxin in complex with orthosteric site-binder CpdA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XR9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	ATX was incubated with each screened compound at a 1:10 (protein:compound) ratio for at least 30 minutes. Crystals were grown for at least 7 days in a 24-well optimization screen: 18 to 20% PEG 3350, 0.1 to 0.4 M NaSCN, and 0.1 to 0.4 M NH4I.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.662	α = 104.159
b = 62.53	β = 98.572
c = 63.638	γ = 93.153

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	PIXEL	DECTRIS PILATUS 2M-F		2020-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999995	SLS	X06DA

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	2	43.68	98	0.137	0.194	0.137	0.985	5.6	3.2		52303

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	2	2.05	96.9		0.798	1.129	0.798	0.437		3.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2xr9	2	43.68	52301	2646	97.999	0.204	0.202	0.21	0.2422	0.25	26.899

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]
1.415	1.245	1.265	-1.99	-1.242	0.588

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.592
r_dihedral_angle_4_deg	16.136
r_dihedral_angle_3_deg	12.76
r_dihedral_angle_1_deg	6.853
r_lrange_it	6.454
r_lrange_other	6.386
r_angle_refined_deg	1.218
r_angle_other_deg	1.084
r_mcangle_it	0.728
r_mcangle_other	0.727
r_scangle_it	0.503
r_scangle_other	0.503
r_mcbond_it	0.394
r_mcbond_other	0.389
r_scbond_it	0.362
r_scbond_other	0.362
r_nbd_refined	0.179
r_symmetry_nbd_other	0.17
r_nbd_other	0.168
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.153
r_xyhbond_nbd_refined	0.111
r_metal_ion_refined	0.095
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.046
r_symmetry_xyhbond_nbd_other	0.019
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6391
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	199

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing
MolProbity	model building