3FDN | pdb_00003fdn

Structure-based drug design of novel Aurora kinase A inhibitors: Structure basis for potency and specificity

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	22% PEG400, 0.1mM ammonia sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.613	α = 90
b = 81.613	β = 90
c = 169.145	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	ADSC QUANTUM 315		2007-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1		NSRRC	BL13B1

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	1.9	30	98	0.035	28.94	3.4		27121

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)
	1.9	1.97	99.3		0.467	2.56	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1MQ4	1.9	30	25207	1335	98.17	0.23055	0.22762	0.23	0.28696	0.29	RANDOM	39.695

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]
-1.17	-0.59		-1.17		1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.754
r_dihedral_angle_3_deg	18.344
r_dihedral_angle_4_deg	18.299
r_dihedral_angle_1_deg	6.132
r_scangle_it	3.785
r_scbond_it	2.257
r_mcangle_it	1.724
r_angle_refined_deg	1.413
r_mcbond_it	0.931
r_symmetry_hbond_refined	0.553

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.754
r_dihedral_angle_3_deg	18.344
r_dihedral_angle_4_deg	18.299
r_dihedral_angle_1_deg	6.132
r_scangle_it	3.785
r_scbond_it	2.257
r_mcangle_it	1.724
r_angle_refined_deg	1.413
r_mcbond_it	0.931
r_symmetry_hbond_refined	0.553
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.289
r_nbd_refined	0.245
r_xyhbond_nbd_refined	0.23
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2134
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	30

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

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.