9RVK | pdb_00009rvk

Crystal structure of Aurora-A bound to DBL5

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	0.1M TRIS pH 8.5, 0.1M BICINE pH 8.5, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350, 0.03M Sodium fluoride, 0.03M Sodium bromide, 0.03M Sodium iodide.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.766	α = 90
b = 68.852	β = 90
c = 89.226	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 EIGER2 R 1M		2024-06-29	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	1.789	56.77	99.3	1	10.7	13.6		33504

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	1.79	1.82			0.3

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	1.789	54.569	33458	1671	99.25	0.197	0.1948	0.1926	0.2383	0.2369	39.823

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]
0.436			0.236		-0.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.209
r_dihedral_angle_6_deg	13.076
r_lrange_it	9.968
r_dihedral_angle_2_deg	8.205
r_dihedral_angle_1_deg	6.248
r_scangle_it	5.126
r_scbond_it	3.294
r_mcangle_it	2.918
r_mcbond_it	1.848
r_angle_refined_deg	1.787
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.113
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2587
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	63

Software

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