2XP2 | pdb_00002xp2

Structure of the Human Anaplastic Lymphoma Kinase in Complex with Crizotinib (PF-02341066)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	286	CO-CRYSTALS OF ALK KINASE DOMAIN WITH PF-02341066 WERE OBTAINED AT 13 DEGREES C BY USING HANGING-DROP VAPOR-DIFFUSION. 0.5 MICROLITERS OF 1:3 MOLAR RATIO OF 14.9 MG/ML PROTEIN SOLUTION TO PF02341066 WAS MIXED WITH 0.5 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 7-10% (W/V) MEPEG 5K, 0.1M MES, PH6.0-6.5 AND 0.15M (NH4)2SO4.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.633	α = 90
b = 57.086	β = 90
c = 104.709	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	80	CCD	ADSC CCD		2010-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	1.86	104.71	92.8	0.07	16	5.7		24837		2	18.8

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	1.86	1.96	64		0.33	2	2.3

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	PDB ENTRY 2WGJ	1.9	36.76	23821	1147	95	0.207	0.207	0.2	0.252	0.25	RANDOM	37

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]
-4.18			-6.55		10.73

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.5
c_scangle_it	3.61
c_mcangle_it	2.5
c_scbond_it	2.39
c_mcbond_it	1.56
c_angle_deg	0.8
c_improper_angle_d	0.69
c_bond_d	0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2262
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	30

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
SCALA	data scaling
CNS	phasing