7AUU | pdb_00007auu

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1-nose mutant in complex with InsP6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AUI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	25% PEG 3350, 0.1 M Bis-Tris propane pH 6.5, 0.2 M Sodium nitrate. Protein:precipitant ratio 3:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM InsP6.

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.12	α = 90
b = 62.12	β = 90
c = 92.472	γ = 120

Symmetry
Space Group	P 32 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	KB focusing mirrors	2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.45	46.54	99.9	0.058	0.016	0.999	21.3	12.9		7984			69.364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.55	100		0.624	0.178	0.937	3.2	12.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	7AUI	2.45	46.54	7535	422	99.86	0.2081	0.2057	0.2083	0.2554	0.2546	RANDOM	88.619

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]
-2.84	-1.42		-2.84		9.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.833
r_dihedral_angle_3_deg	18.198
r_dihedral_angle_4_deg	17.509
r_dihedral_angle_1_deg	6.35
r_angle_refined_deg	1.306
r_angle_other_deg	1.087
r_chiral_restr	0.047
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1146
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing
Coot	model building