9GUC | pdb_00009guc

Adhiron-mediated Identification of a Novel and Selective Allosteric Pocket in Aurora Kinase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G1X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291.15	Molecular Dimensions (Morpheous-Fusion)Condition E6 90 mM LiNaK; 1.2 % Cholic acid derivative; 0.1 M Buffer System 2 (0.5M Sodium HEPES; 0.5M MOPS (acid)); 7.5pH; 30 % Precipitant Mix 1 (40% v/v PEG 500 MME; 20 % w/v PEG 20000)

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.92	α = 90
b = 88.92	β = 90
c = 100.05	γ = 120

Symmetry
Space Group	P 31 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	193	PIXEL	DECTRIS PILATUS 6M		2024-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6199	Diamond	I24

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	2.1	41.96	100	1	13.8	19.7		27145

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	2.1	2.14	98.6		0.9

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	2.1	40.662	27145	1299	99.853	0.193	0.1908	0.1929	0.2319	0.1939	42.242

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]
-0.253	-0.127		-0.253		0.821

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.496
r_dihedral_angle_3_deg	13.905
r_dihedral_angle_2_deg	10.835
r_lrange_other	9.433
r_lrange_it	9.431
r_scangle_it	7.517
r_scangle_other	7.515
r_dihedral_angle_1_deg	6.623
r_mcangle_it	5.391
r_mcangle_other	5.39
r_scbond_it	5.035
r_scbond_other	5.034
r_mcbond_it	3.821
r_mcbond_other	3.817
r_angle_refined_deg	1.745
r_dihedral_angle_other_2_deg	1.126
r_angle_other_deg	0.588
r_nbd_other	0.276
r_nbd_refined	0.226
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.126
r_symmetry_nbd_refined	0.12
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2732
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	66

Software

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