2NP8 | pdb_00002np8

Structural Basis for the Inhibition of Aurora A Kinase by a Novel Class of High Affinity Disubstituted Pyrimidine Inhibitors

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MQ4	pdb entry 1MQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	7% (w/v) PEG 400, 2.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.544	α = 90
b = 81.544	β = 90
c = 172.038	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	100	CCD	NOIR-1	Si-monochromator	2006-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.24	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.25	70	99.4	0.076	0.076	8.6	4		16671			51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.33	99.9		0.482	0.482	1.8	4	2001

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1MQ4	2.25	70.53	15822	15822	840	99.21	0.2457	0.2457	0.24421	0.2834	RANDOM	54.602

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]
-1.06	-0.53		-1.06		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.75
r_dihedral_angle_4_deg	22.184
r_dihedral_angle_3_deg	16.707
r_dihedral_angle_1_deg	5.415
r_scangle_it	2.002
r_scbond_it	1.241
r_angle_refined_deg	1.149
r_mcangle_it	0.888
r_mcbond_it	0.498
r_symmetry_vdw_refined	0.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.75
r_dihedral_angle_4_deg	22.184
r_dihedral_angle_3_deg	16.707
r_dihedral_angle_1_deg	5.415
r_scangle_it	2.002
r_scbond_it	1.241
r_angle_refined_deg	1.149
r_mcangle_it	0.888
r_mcbond_it	0.498
r_symmetry_vdw_refined	0.421
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.247
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2105
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	40

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.