8C8C | pdb_00008c8c

Crystal Structure of Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (PI5P4Ka) bound to an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YBX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	24 % PEG smear low 0.04 M CaCl 0.04 M NaFormate 0.1 M Tris pH pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.661	α = 90
b = 84.935	β = 90
c = 128.346	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS 6M-F		2019-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.096	42.504	84.7	0.04	0.056	0.04	0.996	10.3	1.9		19434			38.071

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)
1	2.1	2.16	19.6		0.532	0.753	0.532	0.766	1.4	1.9

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.096	42.504	19422	961	84.206	0.22	0.2165	0.2	0.2819	0.27	51.147

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]
0.964			-0.161		-0.803

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.912
r_dihedral_angle_3_deg	15.452
r_lrange_it	7.694
r_lrange_other	7.681
r_dihedral_angle_2_deg	7.462
r_dihedral_angle_1_deg	6.926
r_scangle_it	6.032
r_scangle_other	6.03
r_mcangle_it	4.848
r_mcangle_other	4.847
r_scbond_it	4.052
r_scbond_other	4.051
r_mcbond_it	3.406
r_mcbond_other	3.406
r_angle_refined_deg	1.461
r_angle_other_deg	0.487
r_nbd_refined	0.218
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.15
r_nbd_other	0.134
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2420
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing