2YAC | pdb_00002yac

Crystal structure of Polo-like kinase 1 in complex with NMS-P937

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		INTERNAL STRUCTURE WITH AMP-PNP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.595	α = 90
b = 66.595	β = 90
c = 154.035	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 4		2007-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.2	57.64	87.8	0.08	11.2	2.8		18237			19.6

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	2.2	2.32	52.9		0.56	2	2.4

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 (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	INTERNAL STRUCTURE WITH AMP-PNP	2.2	28.84	18225	18225	905	87.4	0.213	0.211	0.21	0.255	0.22	RANDOM	38.5

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]
8.47	5.53		8.47		-16.94

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22
c_scangle_it	3.1
c_scbond_it	2.19
c_mcangle_it	2.12
c_mcbond_it	1.33
c_angle_deg	1.2
c_improper_angle_d	0.84
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2353
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	49

Software

Software
Software Name	Purpose
CNX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing