8ARJ | pdb_00008arj

Anaplastic Lymphoma Kinase with a novel carboline inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		286	0.15 M ammonium sulphate, 9-10.5% monomethyl ether poly (ethylene glycol) (MW 5000), and 0.1 M MES buffer pH 5.3 - 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.714	α = 90
b = 56.593	β = 90
c = 103.243	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	DECTRIS PILATUS 6M		2018-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	1.645	46.281	94	0.069	0.076	0.03	0.999	12.7	6.3		26023

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	1.645	1.821	58.7		1.287	1.416	0.583	0.35	1.6	5.7

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	4CLI	1.645	46.281	26023	1349	69.282	0.198	0.1966	0.2	0.2287	0.23	40.512

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]
-0.102			-0.302		0.404

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.118
r_dihedral_angle_2_deg	16.4
r_dihedral_angle_6_deg	16.257
r_lrange_other	10.294
r_lrange_it	10.292
r_scangle_it	6.819
r_scangle_other	6.817
r_dihedral_angle_1_deg	6.297
r_mcangle_it	5.086
r_mcangle_other	5.086
r_scbond_it	4.369
r_scbond_other	4.367
r_mcbond_it	3.312
r_mcbond_other	3.31
r_angle_refined_deg	1.536
r_angle_other_deg	0.525
r_nbd_refined	0.218
r_symmetry_nbd_other	0.198
r_symmetry_nbd_refined	0.192
r_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_refined	0.031
r_chiral_restr_other	0.014
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2119
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing