2AR5 | pdb_00002ar5

Crystal structure of the mammalian C2alpha-PI3 Kinase PX-domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	293	0.1M Maleic acid/NaOH, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.554	α = 90
b = 56.554	β = 90
c = 92.894	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	98	CCD	ADSC QUANTUM 4		2004-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.8	48.8	99.2	0.057		5.4		16365			41.2

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	1.8	1.86	99.9		0.49	2.2

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 1OCS	1.8	48.8	16345	15519	826	99.2	0.223	0.222	0.23	0.244	0.26	RANDOM	42.75

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]
0.52	0.26		0.52		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	13.55
r_scangle_it	5.969
r_mcangle_it	3.982
r_scbond_it	3.853
r_mcbond_it	2.293
r_angle_refined_deg	1.89
r_angle_other_deg	0.979
r_symmetry_vdw_other	0.352
r_nbd_refined	0.271
r_nbd_other	0.257
r_symmetry_vdw_refined	0.249
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.143
r_nbtor_other	0.093
r_symmetry_hbond_refined	0.05
r_bond_refined_d	0.016
r_gen_planes_other	0.016
r_gen_planes_refined	0.015
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	957
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing