1Y8P

Crystal structure of the PDK3-L2 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JM6	PDK2 PDB entry 1JM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.7	73.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.904	α = 90
b = 120.904	β = 90
c = 240.085	γ = 120

Symmetry
Space Group	P 65 2 2

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 310		2003-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97	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	2.62	50	98.4	0.059	30	7.5	31538	31043		-3

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	2.62	2.71	97.2		0.542	2.1	5.1	2970

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDK2 PDB entry 1JM6	2.63	50	31043	29477	1566	98.34	0.20495	0.20495	0.20358	0.2302	RANDOM	66.251

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]
-0.79	-0.39		-0.79		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.041
r_dihedral_angle_3_deg	20.209
r_dihedral_angle_4_deg	17.618
r_dihedral_angle_1_deg	6.37
r_scangle_it	3.572
r_scbond_it	2.201
r_angle_refined_deg	1.731
r_mcangle_it	1.297
r_mcbond_it	0.679
r_nbtor_refined	0.322
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.21
r_metal_ion_refined	0.182
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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_other
r_symmetry_vdw_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	3836
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing