35WJ | pdb_000035wj

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with an inhibitor UNC7467

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5W2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 5 mM compound for 3 days

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.224	α = 90
b = 78.224	β = 90
c = 84.815	γ = 90

Symmetry
Space Group	P 42 21 2

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	RAYONIX MX300-HS		2020-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	1.7	50	99.6	0.053	49.913	12.6		29472

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			0.839	0.86

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	THROUGHOUT	1.7	37.309	29242	1571	98.897	0.208	0.2054	0.2194	0.2485	0.2607	25.734

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]
1.067			1.067		-2.135

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.215
r_lrange_other	16.633
r_dihedral_angle_6_deg	14.716
r_dihedral_angle_3_deg	13.535
r_dihedral_angle_2_deg	11.17
r_scangle_it	8.671
r_scangle_other	8.668
r_mcangle_it	8.314
r_mcangle_other	8.314
r_dihedral_angle_1_deg	6.447
r_rigid_bond_restr	5.947
r_scbond_it	5.751
r_scbond_other	5.751
r_mcbond_it	5.276
r_mcbond_other	5.261
r_angle_refined_deg	1.787
r_angle_other_deg	0.606
r_nbd_refined	0.231
r_nbd_other	0.23
r_xyhbond_nbd_refined	0.224
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.173
r_symmetry_nbd_refined	0.158
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1918
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling