1U54 | pdb_00001u54

Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U46

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	291	PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 200.384	α = 90
b = 42.332	β = 96.28
c = 70.848	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315		2003-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	38.71	98.3	0.058	12.9	3.6		14697

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	97.8		0.319	3.7	3.64

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	1U46	2.8	38.71	14697	684	98.3	0.226	0.222	0.23	0.322	0.31	RANDOM	27.15

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]
0.26		1.56	2.98		-2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.343
r_scangle_it	2.29
r_angle_refined_deg	1.972
r_scbond_it	1.51
r_angle_other_deg	0.912
r_mcangle_it	0.896
r_mcbond_it	0.515
r_symmetry_vdw_other	0.26
r_nbd_refined	0.252
r_nbd_other	0.231
r_symmetry_vdw_refined	0.23
r_xyhbond_nbd_refined	0.188
r_symmetry_hbond_refined	0.128
r_chiral_restr	0.094
r_nbtor_other	0.093
r_metal_ion_refined	0.083
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4217
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing