5KCV | pdb_00005kcv

Crystal structure of allosteric inhibitor, ARQ 092, in complex with autoinhibited form of AKT1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MRV	1MRV, 2UVM
experimental model	PDB	2UVM	1MRV, 2UVM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	16% butanol, 10mM ammonium sulfate, 0.1% 2-mercaptoethanol, 15% ethylene glycol, 50mM Tris, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.72	α = 90
b = 87.62	β = 90
c = 128.79	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	CCD	ADSC QUANTUM 315r		2010-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.09280	NSLS	X29A

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	2.7	50	92.7	0.055	25.5	12		13431

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	1MRV, 2UVM	2.7	8	12090	638	87.54	0.21271	0.20961	0.22	0.2686	0.29	RANDOM	67.735

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]
-0.31			-1.7		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.776
r_dihedral_angle_4_deg	21.066
r_dihedral_angle_3_deg	18.776
r_long_range_B_refined	11.888
r_long_range_B_other	11.887
r_scangle_other	7.824
r_mcangle_it	7.69
r_mcangle_other	7.689
r_dihedral_angle_1_deg	6.672
r_mcbond_other	5.295
r_mcbond_it	5.293
r_scbond_it	5.255
r_scbond_other	5.253
r_angle_refined_deg	1.526
r_angle_other_deg	0.874
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2762
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing