9T4M | pdb_00009t4m

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) N112S mutant in complex with IP6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9T48

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	Protein: 24mg/mL Ip6: 10mM Precipitant condition: 31% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2. Ratio: 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.9	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.131	α = 90
b = 100.131	β = 90
c = 34.06	γ = 120

Symmetry
Space Group	P 61

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 4M		2023-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.96770	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.78	50.07	100	0.13	0.99	4.5	15.9		19071			18.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81			6.95	0.33	0.1

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	1.78	50.07	19071	861	99.953	0.189	0.1867	0.1954	0.2421	0.2439	22.887

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]
0.183	0.092		0.183		-0.594

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.511
r_dihedral_angle_3_deg	12.789
r_dihedral_angle_2_deg	9.957
r_lrange_it	8.312
r_lrange_other	8.21
r_dihedral_angle_1_deg	6.867
r_scangle_it	5.196
r_scangle_other	5.191
r_mcangle_it	3.38
r_mcangle_other	3.379
r_scbond_it	3.252
r_scbond_other	3.133
r_mcbond_it	2.071
r_mcbond_other	2.071
r_angle_refined_deg	1.667
r_angle_other_deg	0.558
r_symmetry_nbd_refined	0.257
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.189
r_nbd_other	0.181
r_nbtor_refined	0.174
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.075
r_metal_ion_refined	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1200
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	48

Software

Software
Software Name	Purpose
autoPROC	data processing
MOLREP	phasing
REFMAC	refinement
Coot	model building
autoPROC	data reduction
autoPROC	data scaling
REFMAC	phasing