3DBE

Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 557

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 22.5% PEG 3350, and 15% glycerol; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136	α = 90
b = 136	β = 90
c = 136	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	160	CCD	ADSC QUANTUM 315		2007-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.98	SSRL	BL9-1

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	3.32	30	99.4	0.091	7.4	3.8		6290

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)
	3.32	3.5	99.9		0.394	1.9

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	3d5w	3.32	30	5498	792	99.35	0.23676	0.2318	0.2699	RANDOM	74.57

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.671
r_dihedral_angle_3_deg	16.864
r_dihedral_angle_4_deg	10.231
r_dihedral_angle_1_deg	4.935
r_mcangle_it	3.463
r_scangle_it	2.695
r_mcbond_it	2.02
r_scbond_it	1.419
r_angle_refined_deg	1.175
r_nbtor_refined	0.304
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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	2262
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing