8XPG | pdb_00008xpg

The Crystal Structure of polo box domain of Plk4 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N9J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.00M Ammonium sulfate, 100mM TRIS, pH7.0, 200mM Lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.304	α = 90
b = 77.614	β = 90
c = 120.644	γ = 90

Symmetry
Space Group	P 21 2 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	PIXEL	DECTRIS PILATUS 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	2.7	48.59	100	0.106	15.1	9.1		16692

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	2.7	2.83			1.031

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	2.7	48	16663	861	99.922	0.211	0.2086	0.21	0.2603	0.26	63.247

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]
-1.477			1.442		0.034

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.228
r_dihedral_angle_3_deg	12.047
r_lrange_it	8.975
r_lrange_other	8.965
r_dihedral_angle_1_deg	6.845
r_scangle_it	5.313
r_scangle_other	5.292
r_mcangle_it	5.277
r_mcangle_other	5.276
r_dihedral_angle_2_deg	4.479
r_mcbond_it	3.193
r_mcbond_other	3.193
r_scbond_it	3.171
r_scbond_other	3.136
r_angle_refined_deg	0.874
r_angle_other_deg	0.296
r_nbd_refined	0.191
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.172
r_xyhbond_nbd_refined	0.151
r_nbd_other	0.128
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.038
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3639
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	40

Software

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