9S0W | pdb_00009s0w

Crystal structure of Aurora-A bound to DBL3

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	0.09M Halides, 0.12M Ethyleneglycol, 0.1M Buffer system 1, 37.5% Precipitant mix 4

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.27	α = 90
b = 91.32	β = 90
c = 111.19	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		2025-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.07	47.49	100	1	14.5	13.3		25854

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	2.07	2.11			0.4

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	2.07	47.49	25772	1317	99.88	0.229	0.2271	0.228	0.2669	0.2666	48.405

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]
4.96			-6.3		1.339

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.463
r_dihedral_angle_3_deg	13.273
r_dihedral_angle_1_deg	6.307
r_lrange_it	4.072
r_lrange_other	4.061
r_scangle_it	2.406
r_scangle_other	2.405
r_mcangle_other	2.073
r_mcangle_it	2.071
r_scbond_it	1.41
r_scbond_other	1.406
r_mcbond_it	1.274
r_mcbond_other	1.273
r_angle_refined_deg	0.888
r_angle_other_deg	0.341
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.195
r_nbd_other	0.181
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.128
r_xyhbond_nbd_refined	0.112
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.04
r_dihedral_angle_other_2_deg	0.023
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2664
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
MOLREP	phasing
PDB-REDO	refinement