9S0K | pdb_00009s0k

Crystal structure of Aurora-A bound to DBL1

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	2.4M di-Sodium malonate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.769	α = 90
b = 86.033	β = 90
c = 94.182	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	63.52	78.3	1	20.7	9.3		13349

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	2.362	63.52	13349	669	77.719	0.204	0.2011	0.2026	0.2498	0.2582	20.838

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]
0.338			0.02		-0.358

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.162
r_dihedral_angle_6_deg	13.098
r_lrange_other	8.284
r_lrange_it	8.283
r_dihedral_angle_1_deg	8.263
r_scangle_it	5.873
r_scangle_other	5.871
r_mcangle_other	4.251
r_mcangle_it	4.25
r_scbond_it	3.674
r_scbond_other	3.674
r_mcbond_other	2.68
r_mcbond_it	2.679
r_angle_refined_deg	0.916
r_dihedral_angle_other_2_deg	0.771
r_angle_other_deg	0.344
r_nbd_refined	0.195
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.169
r_nbd_other	0.162
r_symmetry_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.136
r_xyhbond_nbd_refined	0.128
r_metal_ion_refined	0.121
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.042
r_bond_refined_d	0.005
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	2577
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	28

Software

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