8SC8 | pdb_00008sc8

Structure of PI3KG in complex with MTX-531

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	293	0.2 M Lithium Sulfate, 0.1 M TRIS-HCl pH 8.2, 15% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.934	α = 90
b = 67.452	β = 95.274
c = 106.983	γ = 90

Symmetry
Space Group	C 1 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	100	PIXEL	DECTRIS PILATUS3 2M		2022-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.687	33.726	91.6	0.0717	0.0785	0.0316	0.998	13.96	6.1		23452

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.687	2.975	53.7		1.2206	1.3377	0.5414	0.547	1.34	6.05	2346

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	2.687	33.726	23452	1194	81.564	0.198	0.1951	0.2	0.2533	0.26	98.219

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]
-2.476		-1.306	0.87		1.816

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.885
r_dihedral_angle_6_deg	13.013
r_lrange_it	6.767
r_lrange_other	6.766
r_dihedral_angle_1_deg	6.225
r_mcangle_it	4.367
r_mcangle_other	4.367
r_scangle_it	3.72
r_scangle_other	3.72
r_dihedral_angle_2_deg	3.283
r_mcbond_it	2.538
r_mcbond_other	2.536
r_scbond_it	2.151
r_scbond_other	2.151
r_angle_refined_deg	0.812
r_angle_other_deg	0.283
r_nbd_refined	0.187
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.137
r_nbd_other	0.116
r_symmetry_nbd_refined	0.106
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_refined	0.038
r_chiral_restr	0.037
r_symmetry_xyhbond_nbd_other	0.007
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6708
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	56

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
REFMAC	refinement
REFMAC	phasing