3LS8 | pdb_00003ls8

Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IHY	PDB ENTRY 3IHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25% PEG3350, 0.2M ammonium acetate, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.686	α = 90
b = 141.151	β = 90
c = 163.975	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 315	mirrors	2009-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97890	Diamond	I04

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	70.9	99.3	0.092	0.092	12.4	4.8	68403	68403			31.439

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	2.37	95.8		0.451	0.451	1.5	2.8	9539

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 3IHY	2.25	70.9	64837	64837	3491	99.26	0.21078	0.20862	0.2	0.2507	0.24	RANDOM	29.677

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]
-1.91			-0.63		2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.536
r_dihedral_angle_4_deg	20.025
r_dihedral_angle_3_deg	14.879
r_dihedral_angle_1_deg	4.885
r_scangle_it	2.046
r_scbond_it	1.251
r_angle_refined_deg	1.068
r_angle_other_deg	0.853
r_mcangle_it	0.737
r_mcbond_it	0.376

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.536
r_dihedral_angle_4_deg	20.025
r_dihedral_angle_3_deg	14.879
r_dihedral_angle_1_deg	4.885
r_scangle_it	2.046
r_scbond_it	1.251
r_angle_refined_deg	1.068
r_angle_other_deg	0.853
r_mcangle_it	0.737
r_mcbond_it	0.376
r_mcbond_other	0.076
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8713
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	54

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	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.