4WHH | pdb_00004whh

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RQ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M HEPES, 2.0M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.927	α = 90
b = 58.3	β = 90
c = 66.753	γ = 90

Symmetry
Space Group	P 21 21 21

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		2014-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	1.9	50	97.6	0.069	15.1	11.5		18067

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	1.9	1.93	100		0.434		11.7	914

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	3RQ7	1.9	43.91	18067	904	97.25	0.1928	0.1907	0.2	0.2361	0.25	RANDOM	32.986

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]
-1.37			-0.97		2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.939
r_dihedral_angle_3_deg	14.644
r_dihedral_angle_4_deg	13.453
r_dihedral_angle_1_deg	6.076
r_mcangle_it	4.101
r_mcbond_other	2.93
r_mcbond_it	2.929
r_angle_refined_deg	1.989
r_angle_other_deg	1.36
r_chiral_restr	0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.939
r_dihedral_angle_3_deg	14.644
r_dihedral_angle_4_deg	13.453
r_dihedral_angle_1_deg	6.076
r_mcangle_it	4.101
r_mcbond_other	2.93
r_mcbond_it	2.929
r_angle_refined_deg	1.989
r_angle_other_deg	1.36
r_chiral_restr	0.11
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1754
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	11

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.