9SV0 | pdb_00009sv0

Crystal structure of Aurora-A bound to DBS4

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 NPS, 0.1M Buffer system 2 pH 7.5, 30% Precipitant mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.33	α = 90
b = 88.33	β = 90
c = 240.29	γ = 90

Symmetry
Space Group	P 41 21 2

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		2024-11-22	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	2.23	60.45	99.9	1	14.1	26.4		47348

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	2.27			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	2.23	60.45	47251	2318	99.698	0.204	0.2014	0.2087	0.2493	0.2549	62.602

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]
-0.349			-0.349		0.697

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.387
r_dihedral_angle_3_deg	12.757
r_lrange_other	11.255
r_lrange_it	11.25
r_dihedral_angle_2_deg	9.461
r_scangle_it	8.913
r_scangle_other	8.887
r_mcangle_it	7.279
r_mcangle_other	7.278
r_dihedral_angle_1_deg	6.226
r_scbond_it	6.181
r_scbond_other	6.169
r_mcbond_it	5.246
r_mcbond_other	5.239
r_angle_refined_deg	1.306
r_angle_other_deg	0.469
r_nbd_refined	0.216
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.167
r_nbd_other	0.153
r_metal_ion_refined	0.101
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_2	0.08
r_chiral_restr	0.066
r_dihedral_angle_other_2_deg	0.02
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	5039
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	87

Software

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