9R8C | pdb_00009r8c

CRYSTAL STRUCTURE OF WILD-TYPE PLK1 KINASE DOMAIN IN COMPLEX WITH THIAZOLIDINONE INHIBITOR COMPOUND 1 AND A SELECTIVE DARPIN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	303	0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.605	α = 90
b = 135.302	β = 90
c = 136.7	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	100	CCD	ADSC QUANTUM 315		2006-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.037	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.24	96.16	97.9	0.084	14.6	4.2		233157			40.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.24	2.38	90.7		1.118	1.2	3.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.243	48.128	55347	2826	98.06	0.191	0.1882	0.1928	0.236	0.2351	50.407

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]
0.604			-0.436		-0.168

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.088
r_dihedral_angle_3_deg	12.776
r_lrange_other	10.339
r_lrange_it	10.332
r_scangle_it	8.471
r_scangle_other	8.47
r_dihedral_angle_2_deg	7.278
r_mcangle_other	6.802
r_mcangle_it	6.796
r_dihedral_angle_1_deg	6.41
r_scbond_it	6.044
r_scbond_other	6.044
r_mcbond_it	4.876
r_mcbond_other	4.876
r_angle_refined_deg	1.352
r_angle_other_deg	0.505
r_symmetry_nbd_refined	0.296
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.191
r_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.148
r_ncsr_local_group_1	0.125
r_ncsr_local_group_2	0.093
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.069
r_chiral_restr_other	0.032
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6620
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing