9S14 | pdb_00009s14

Crystal structure of Aurora-A bound to DBS1

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	4M Sodium nitrate, 0.1M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.61	α = 90
b = 77.42	β = 90
c = 84.24	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		2024-10-22	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	51.27	98.9	1	13.8	13.6		28883

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	2.03			0.4

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	51.267	28848	1300	98.771	0.189	0.187	0.1994	0.228	0.2374	57.563

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]
2.639			-0.7		-1.938

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.242
r_dihedral_angle_3_deg	12.764
r_lrange_other	8.857
r_lrange_it	8.85
r_dihedral_angle_2_deg	7.047
r_scangle_it	6.969
r_scangle_other	6.967
r_dihedral_angle_1_deg	5.776
r_scbond_it	4.341
r_scbond_other	4.341
r_mcangle_it	4.185
r_mcangle_other	4.184
r_mcbond_it	2.835
r_mcbond_other	2.835
r_angle_refined_deg	1.191
r_dihedral_angle_other_2_deg	0.461
r_angle_other_deg	0.395
r_nbd_refined	0.213
r_symmetry_nbd_other	0.184
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.174
r_nbd_other	0.172
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2935
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	27

Software

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