9S7T | pdb_00009s7t

Crystal structure of Aurora-A bound to DBS5

X-RAY DIFFRACTION

---

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	0.06M Divalents cation 1, 2.5% Cryo-polyol, 0.1M Buffer system 3, 30% Precipitant mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.09	α = 90
b = 87.09	β = 90
c = 215.26	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 EIGER2 X 16M		2024-12-14	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	2.23	71.67	92.4	1	13.9	16		41554

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	2.23	2.41			0.7

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	2.28	71.67	41503	2155	94.152	0.192	0.19	0.1972	0.2313	0.2368	69.528

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]
-1.21	-0.605		-1.21		3.925

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.547
r_dihedral_angle_6_deg	13.526
r_lrange_other	10.338
r_lrange_it	10.328
r_scangle_it	8.512
r_scangle_other	8.511
r_dihedral_angle_2_deg	7.714
r_dihedral_angle_1_deg	6.3
r_mcangle_it	6.285
r_mcangle_other	6.285
r_scbond_it	5.693
r_scbond_other	5.692
r_mcbond_it	4.452
r_mcbond_other	4.448
r_angle_refined_deg	1.323
r_angle_other_deg	0.458
r_dihedral_angle_other_2_deg	0.437
r_symmetry_nbd_refined	0.395
r_nbd_refined	0.208
r_nbd_other	0.204
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.159
r_ncsr_local_group_2	0.104
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_1	0.069
r_chiral_restr	0.062
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5606
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing