8XB9 | pdb_00008xb9

The Crystal Structure of polo-box domain 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	6AX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	31% PEG3350, 0.1M Bis Tris pH 5.8

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.181	α = 90
b = 92.786	β = 101.642
c = 35.89	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2021-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000000	SPring-8	BL45XU

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	1.95	46.39	98.1	0.051	12.7	5.2		15223

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	1.95	2			0.328

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	1.95	35.176	15199	756	97.894	0.191	0.1885	0.2	0.2448	0.25	44.155

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]
-0.258		1.802	-0.381		-0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.442
r_dihedral_angle_6_deg	15.279
r_dihedral_angle_2_deg	11.373
r_lrange_other	9.715
r_lrange_it	9.701
r_scangle_it	6.96
r_scangle_other	6.958
r_dihedral_angle_1_deg	6.837
r_mcangle_it	5.502
r_mcangle_other	5.5
r_scbond_it	4.596
r_scbond_other	4.595
r_mcbond_it	4.024
r_mcbond_other	4.016
r_angle_refined_deg	1.423
r_angle_other_deg	0.468
r_symmetry_xyhbond_nbd_refined	0.316
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.204
r_symmetry_nbd_other	0.197
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.178
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.053
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1803
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	4

Software

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