3D5U | pdb_00003d5u

Crystal structure of a wildtype Polo-like kinase 1 (Plk1) catalytic domain.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D5W	pdb entry 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 tri-sodium citrate pH 5.6, 0.2 M (NH4)2SO4, and 25% PEG 3350; cryoprotectant: paraffin oil., VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.841	α = 90
b = 135.841	β = 90
c = 135.841	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	180	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	2.8	30	96.7	0.075	7.4	4.9		9961

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)
	2.8	2.95	98.3		0.39	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 (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 3d5w	2.8	30	8970	988	95.61	0.23105	0.22543	0.22	0.28127	0.28	RANDOM	60.537

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	30.936
r_dihedral_angle_3_deg	13.824
r_dihedral_angle_4_deg	11.868
r_dihedral_angle_1_deg	3.848
r_mcangle_it	2.2
r_scangle_it	1.502
r_mcbond_it	1.268
r_scbond_it	0.88
r_angle_refined_deg	0.823
r_nbtor_refined	0.294
r_nbd_refined	0.161
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.105
r_symmetry_vdw_refined	0.102
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	2300
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing