7AUR | pdb_00007aur

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in complex with AMP-PNP

X-RAY DIFFRACTION

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	5	291	25% PEG 6000, 0.1 M Sodium acetate pH 5.0, 0.1 M NaCl. Protein:precipitant ratio 2:1. Protein buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 1 mM DTT, 10 mM AMP-PNP.

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.958	α = 90
b = 61.958	β = 90
c = 95.924	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	2018-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979300	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	1.65	47.96	99.8	0.083	0.02	0.999	18.9	19		26240			27.77

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	1.65	1.68	99.8		0.666	0.164	0.937	4.8	17.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	7AUI	1.65	46.87	24867	1336	99.8	0.2106	0.209	0.22	0.242	0.24	RANDOM	35.977

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]
0.14	0.07		0.14		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.579
r_dihedral_angle_3_deg	13.725
r_dihedral_angle_4_deg	10.445
r_dihedral_angle_1_deg	6.796
r_angle_refined_deg	1.512
r_angle_other_deg	1.301
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.579
r_dihedral_angle_3_deg	13.725
r_dihedral_angle_4_deg	10.445
r_dihedral_angle_1_deg	6.796
r_angle_refined_deg	1.512
r_angle_other_deg	1.301
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1158
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	96

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.