2V5Q | pdb_00002v5q

CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH 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	1OL5	PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141
experimental model	PDB	3H10	PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141
experimental model	PDB	1MJ0	PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			303	0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.329	α = 90
b = 135.225	β = 90
c = 136.824	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 CCD	MIRRORS	2006-07-20	M	SINGLE WAVELENGTH

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

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	2.3	96.2	99.3	0.06	15.7	3.5		51702			45.7

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	2.3	2.42	99.3		0.4	3.3	3.6

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141	2.3	61.08	49051	2601	98.9	0.184	0.182	0.224	RANDOM	34.28

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]
1.07			-1.87		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.477
r_dihedral_angle_4_deg	18.875
r_dihedral_angle_3_deg	15.116
r_scangle_it	7.068
r_dihedral_angle_1_deg	5.952
r_scbond_it	5.214
r_mcangle_it	2.8
r_mcbond_it	1.615
r_angle_refined_deg	1.265
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6502
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms

Software

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