9S1G | pdb_00009s1g

Crystal structure of Aurora-A bound to DBL6

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	0.8% Alkaloids, 0.12M Ethyleneglycol, 0.1M Buffer system 3 pH 8.5, 30% Precipitant mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.735	α = 90
b = 75.483	β = 90
c = 87.736	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	2.355	57.22	78.5	1	28.2	8.3		12251

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	2.52			1

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	2.355	57.22	12251	635	78.457	0.2	0.1965	0.2051	0.2585	0.2599	37.692

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]
0.157			-0.361		0.204

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.729
r_dihedral_angle_6_deg	10.895
r_dihedral_angle_1_deg	5.979
r_dihedral_angle_2_deg	5.964
r_lrange_it	5.825
r_lrange_other	5.812
r_scangle_it	3.709
r_scangle_other	3.709
r_mcangle_other	3.165
r_mcangle_it	3.164
r_scbond_it	2.154
r_scbond_other	2.153
r_mcbond_it	1.829
r_mcbond_other	1.828
r_angle_refined_deg	0.947
r_angle_other_deg	0.334
r_symmetry_nbd_refined	0.219
r_dihedral_angle_other_2_deg	0.204
r_nbd_refined	0.198
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.157
r_nbd_other	0.14
r_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.045
r_gen_planes_refined	0.003
r_bond_refined_d	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	2527
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	28

Software

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