9T4E | pdb_00009t4e

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	Protein: 20mg/mL Precipitant condition: 17% PEG 6K, 20mM NaF, 1mM ZnCl, 0.1M Hepes pH 7, 10 mM Na6[(PO3)6] Ratio: 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.942	α = 90
b = 59.942	β = 90
c = 83.078	γ = 120

Symmetry
Space Group	P 31 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 PILATUS 6M		2022-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

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	1.54	51.91	84.4	0.01	0.99	25.7	12.7		19582			29.7

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	1.54	1.63			0.46	0.59	1.1

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.541	51.91	19582	918	75.033	0.201	0.1989	0.2068	0.2339	0.2418	32.669

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]
-0.026	-0.013		-0.026		0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.936
r_dihedral_angle_3_deg	12.711
r_dihedral_angle_2_deg	10.835
r_lrange_it	9.346
r_lrange_other	9.301
r_scangle_it	7.402
r_scangle_other	7.133
r_dihedral_angle_1_deg	7.125
r_scbond_it	4.833
r_scbond_other	4.577
r_mcangle_other	4.44
r_mcangle_it	4.438
r_mcbond_it	3.233
r_mcbond_other	3.217
r_angle_refined_deg	1.808
r_angle_other_deg	0.611
r_xyhbond_nbd_refined	0.221
r_nbd_other	0.219
r_nbd_refined	0.21
r_symmetry_nbd_other	0.199
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.16
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1025
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	21

Software

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