9SQ7 | pdb_00009sq7

Crystal structure of Aurora-A bound to DBS2

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	0.12 M Alcohols, 0. 1M Buffer system 3 pH 8.5, 30 % Precipitant mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.049	α = 90
b = 84.049	β = 90
c = 201.105	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	199	PIXEL	DECTRIS EIGER2 X 16M		2024-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.899	58.961	99.9	1	29.6	16.6		18955

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	2.9	2.95			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	2.899	58.961	18914	908	99.71	0.206	0.2038	0.2062	0.2439	0.2414	52.77

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]
-2.119	-1.06		-2.119		6.875

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_6_deg	12.505
r_dihedral_angle_1_deg	6.216
r_dihedral_angle_2_deg	5.197
r_lrange_it	2.82
r_lrange_other	2.813
r_dihedral_angle_other_2_deg	1.592
r_mcangle_it	1.023
r_mcangle_other	1.023
r_scangle_it	1.015
r_scangle_other	1.015
r_angle_refined_deg	0.98
r_mcbond_it	0.582
r_mcbond_other	0.581
r_scbond_it	0.573
r_scbond_other	0.573
r_angle_other_deg	0.361
r_symmetry_xyhbond_nbd_refined	0.282
r_symmetry_nbd_refined	0.216
r_nbd_other	0.208
r_nbd_refined	0.206
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.121
r_ncsr_local_group_1	0.117
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_2	0.063
r_metal_ion_refined	0.06
r_chiral_restr	0.046
r_bond_refined_d	0.003
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	5094
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	58

Software

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