9S61 | pdb_00009s61

Crystal structure of Aurora-A bound to DBL8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.09 M NPS, 0.12M Ethylene glycol, 0.1 M Buffer system 3 pH 8.5, 37.5% Precipitant mix 4

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.392	α = 90
b = 71.759	β = 90
c = 88.879	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	PIXEL	DECTRIS EIGER X 16M		2024-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.36	55.833	78.9	1	19.3	9.5		11954

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.54			0.6

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	2.369	55.833	11953	564	77.101	0.19	0.1866	0.195	0.2596	0.2584	42.929

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]
-0.245			-0.409		0.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.152
r_dihedral_angle_6_deg	11.555
r_dihedral_angle_1_deg	6.118
r_lrange_it	5.989
r_lrange_other	5.983
r_dihedral_angle_2_deg	5.284
r_scangle_it	4.135
r_scangle_other	4.134
r_mcangle_it	3.534
r_mcangle_other	3.533
r_scbond_it	2.396
r_scbond_other	2.396
r_mcbond_it	2.104
r_mcbond_other	2.103
r_angle_refined_deg	1.101
r_symmetry_xyhbond_nbd_refined	0.451
r_angle_other_deg	0.384
r_nbd_refined	0.199
r_symmetry_nbd_refined	0.188
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.139
r_nbd_other	0.133
r_dihedral_angle_other_2_deg	0.084
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.053
r_symmetry_xyhbond_nbd_other	0.023
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	2472
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
MOLREP	phasing
STARANISO	data scaling