3DJ7 | pdb_00003dj7

Crystal structure of the mouse Aurora-A catalytic domain (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with Compound 130.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D14	PDB entry 3d14

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.9	293	Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 1.0 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 6.9; temperature: 293K; cryoprotectant: tacsimate; crystal frozen by immersion in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.75	α = 90
b = 82.75	β = 90
c = 169.728	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	160	IMAGE PLATE	RIGAKU RAXIS IV		2008-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	30	99.2	0.051	19.3	7	9056	8957

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.86	99.9		0.314	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3d14	2.8	22.83	8957	8016	888	98.48	0.26872	0.26571	0.26	0.29553	0.29	RANDOM	68.529

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]
-1.68	-0.84		-1.68		2.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.56
r_dihedral_angle_3_deg	15.132
r_dihedral_angle_4_deg	14.186
r_dihedral_angle_1_deg	4.583
r_mcangle_it	2.259
r_scangle_it	1.59
r_mcbond_it	1.31
r_angle_refined_deg	0.963
r_scbond_it	0.94
r_nbtor_refined	0.295
r_nbd_refined	0.166
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.105
r_symmetry_hbond_refined	0.083
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2065
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing