2ZKJ

Crystal structure of human PDK4-ADP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y8N	PDB entry 1Y8N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.9M ammonium sulfate, 4% polyethylene glycol 400, 100mM potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.616	α = 90
b = 68.743	β = 100.1
c = 81.554	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 315	mirrrors	2008-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-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	2	50	99.6	0.056	23.4	4.1		52354

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)
	2	2.03	100		0.665	2.4	4.2	2631

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1Y8N	2	49.22	49635	2668	99.37	0.18771	0.18488	0.24016	RANDOM	41.96

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]
-0.21		-0.2	1.08		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.923
r_dihedral_angle_4_deg	21.24
r_dihedral_angle_3_deg	16.176
r_dihedral_angle_1_deg	5.851
r_scangle_it	4.52
r_scbond_it	3.165
r_mcangle_it	1.842
r_angle_refined_deg	1.831
r_mcbond_it	1.387
r_nbtor_refined	0.317
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.224
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.135
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	5737
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing