4WHL | pdb_00004whl

A New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	293	0.1M Citric acid, 28% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.76	α = 90
b = 57.76	β = 90
c = 137.568	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 270		2013-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	1.0000	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	50	99.9	8.8	16.4		6904

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.71	50	6519	340	99.91	0.1854	0.1822	0.19	0.2454	0.19	RANDOM	47.345

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]
-1.69			-1.69		3.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.625
r_dihedral_angle_3_deg	20.923
r_dihedral_angle_4_deg	18.809
r_dihedral_angle_1_deg	7.917
r_mcangle_it	5.456
r_mcbond_other	3.455
r_mcbond_it	3.453
r_angle_refined_deg	1.627
r_angle_other_deg	1.075
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.625
r_dihedral_angle_3_deg	20.923
r_dihedral_angle_4_deg	18.809
r_dihedral_angle_1_deg	7.917
r_mcangle_it	5.456
r_mcbond_other	3.455
r_mcbond_it	3.453
r_angle_refined_deg	1.627
r_angle_other_deg	1.075
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1775
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	56

Software

Software
Software Name	Purpose
HKL-2000	data reduction
ADSC	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.