7AUS | pdb_00007aus

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with P15

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	4.5	291	16% PEG 3350, 0.1 M Sodium acetate pH 4.5, 0.1 M NaCl, 5 mM Magnesium chloride, 20 mM Sodium fluoride. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM Sodium hexametaphosphate.

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.67	α = 90
b = 61.67	β = 90
c = 95.73	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	2019-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979182	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	1.75	47.87	100	0.047	0.011	0.998	34.3	18.9		21864			33.348

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	1.75	1.78	100		0.652	0.149	0.948	5	19.8

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	1.75	46.68	20721	1105	99.97	0.243	0.241	0.2473	0.2792	0.2828	RANDOM	44.273

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]
0.27	0.13		0.27		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.987
r_dihedral_angle_4_deg	19.775
r_dihedral_angle_3_deg	16.371
r_dihedral_angle_1_deg	6.74
r_angle_refined_deg	1.42
r_angle_other_deg	1.187
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1356
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	62

Software

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