9GCF | pdb_00009gcf

HUMAN PI3KDELTA IN COMPLEX WITH ISOCUMARIN INHIBITOR CHF-6523

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	16% PEG6000, 0.10 M KCL, 0.10 M MES

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.324	α = 90
b = 108.45	β = 90
c = 142.16	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	PIXEL	DECTRIS EIGER X 16M		2016-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00000	SLS	X06SA

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	2.89	86.22	96.9	0.033	20.67	3.1		30965

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	2.89	3.13			0.449

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 (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	2.89	86.22	30324	641	96.87	0.23007	0.22869	0.2276	0.29637	0.2908	RANDOM	102.289

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]
4.15			3.13		-7.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.981
r_long_range_B_refined	17.809
r_long_range_B_other	17.808
r_scangle_other	14.782
r_mcangle_it	14.314
r_mcangle_other	14.313
r_dihedral_angle_4_deg	12.088
r_dihedral_angle_3_deg	11.331
r_scbond_it	10.159
r_scbond_other	10.159
r_mcbond_other	9.977
r_mcbond_it	9.976
r_dihedral_angle_1_deg	4.719
r_angle_refined_deg	0.967
r_angle_other_deg	0.837
r_chiral_restr	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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	8843
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
MOLREP	phasing