6BDN | pdb_00006bdn

Crystal structure of human TAO3 kinase binding ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U5R	PDB entry 1U5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		279.15	Drops: 1.8 uL protein + 1.0 uL well solution, protein solution: 6.5 mg/mL TAO3K in 0.7 mM ADP, 5 mM magnesium chloride, 100 mM sodium chloride, 25 mM Tris, pH 8.0, 2 mM BME, 0.3 mM EDTA, well solution: 20% PEG3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, cryoprotectant: 20% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.187	α = 90
b = 59.897	β = 90
c = 110.177	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	CCD	ADSC QUANTUM 315r		2015-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12708	SSRL	BL7-1

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	1.5	38.1	99.8	0.037	0.042	0.02	0.999	17.1	4.4		59157

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	1.5	1.53	99.8		0.617	0.701	0.327	0.751		4.4

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 1U5R	1.5	38.1	56151	2959	99.71	0.187	0.1856	0.19	0.2145	0.22	RANDOM	24.183

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]
-0.54			0.55		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.296
r_dihedral_angle_4_deg	20.125
r_dihedral_angle_3_deg	14.112
r_dihedral_angle_1_deg	6.277
r_angle_refined_deg	2.383
r_angle_other_deg	1.164
r_chiral_restr	0.146
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2473
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	47

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing