8X72 | pdb_00008x72

The Crystal Structure of PLK1 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.5M MgAc2, 12% PEG 4000, 0.3mM ZnAc2

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.5	α = 90
b = 67.5	β = 90
c = 153.347	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	PIXEL	DECTRIS EIGER X 16M		2023-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95365	Australian Synchrotron	MX2

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	46.53	96.2	0.111	12.5	11		20455

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	2.27			1.003

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	FREE R-VALUE	2.2	46.53	20408	963	95.947	0.198	0.195	0.2	0.2497	0.25	46.856

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]
1.53	0.765		1.53		-4.964

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.842
r_dihedral_angle_3_deg	13.55
r_dihedral_angle_4_deg	12.73
r_dihedral_angle_1_deg	6.519
r_lrange_it	6.036
r_lrange_other	6.015
r_scangle_it	4.081
r_scangle_other	4.08
r_mcangle_it	3.45
r_mcangle_other	3.449
r_scbond_it	2.458
r_scbond_other	2.458
r_mcbond_it	2.146
r_mcbond_other	2.142
r_angle_refined_deg	1.241
r_angle_other_deg	1.099
r_symmetry_nbd_refined	0.265
r_nbd_other	0.209
r_nbd_refined	0.188
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.157
r_chiral_restr_other	0.129
r_xyhbond_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.087
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2379
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	66

Software

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