1U4D | pdb_00001u4d

Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	291	PEG 2000, sodium chloride, magnesium chloride, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.552	α = 90
b = 42.918	β = 112.02
c = 85.149	γ = 90

Symmetry
Space Group	P 1 21 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 4		2003-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	2.1	46.6	99.7	0.059	14.6	3.5		32292

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)
	2.1	2.21	98.3		0.373	2.6	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 CODE 1U46	2.1	46.6	32292	30671	1621	99.7	0.205	0.203	0.21	0.248	0.24	RANDOM	35.67

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]
-2.12		-2.1	2.34		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.871
r_scangle_it	3.829
r_scbond_it	2.414
r_mcangle_it	1.852
r_angle_refined_deg	1.81
r_mcbond_it	1.026
r_angle_other_deg	0.927
r_symmetry_vdw_other	0.32
r_symmetry_vdw_refined	0.315
r_nbd_other	0.24
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.098
r_nbtor_other	0.085
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
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_refined
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	4168
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing