2OU7 | pdb_00002ou7

Structure of the Catalytic Domain of Human Polo-like Kinase 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MQ4	PDB entry 1MQ4 (residues 274-307 deleted).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	Protein buffer: 50 mM HEPES, pH 7.5, 5 mM TCEP. Protein was incubated on ice with 5 mM ligand (1:20 dilution of 100 mM stock in H2O for AMPPNP or DMSO for PHA-680626) for 0.5-1 h, followed by a brief centrifugation step and drop setting at RT (0.5 microliter protein + 0.5 microliter reservoir solution consisting of 500 mM magnesium acetate, 10 % PEG 4000 and 0.3 mM zinc acetate for AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.958	α = 90
b = 65.958	β = 90
c = 154.045	γ = 120

Symmetry
Space Group	P 32 2 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 210		2006-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	45.9		0.063	23.26	5.6		14898

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	71.6		0.319	1.85	3.9	817

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 1MQ4 (residues 274-307 deleted).	2.4	45.9	14116	757	93.98	0.20463	0.20302	0.29	0.23534	0.3	RANDOM	22.44

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]
4.25	2.12		4.25		-6.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.08
r_scangle_it	1.823
r_angle_refined_deg	1.246
r_scbond_it	1.051
r_angle_other_deg	0.887
r_mcangle_it	0.796
r_mcbond_it	0.421
r_symmetry_hbond_refined	0.374
r_nbd_other	0.217
r_symmetry_vdw_other	0.212
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.149
r_nbtor_other	0.082
r_metal_ion_refined	0.042
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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	2366
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing