Experiment: 7SDB

Structure of the PTP-like myo-inositol phosphatase from Legionella pneumophila str. Paris in complex with myo-inositol hexakisphosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	100 mM Tris HCl (7.4), 12% PEG 4000, 40 mM magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.309	α = 90
b = 62.456	β = 90
c = 95.497	γ = 90

Symmetry
Space Group	P 21 21 21

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 200K		2021-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU MICROMAX-003	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	24.08	97.5	0.071	17.81	3.5		25244			15.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07			0.198		3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4TVV	2	24.08	1.34	25199	1999	97.58	0.1636	0.1605	0.1603	0.199	0.2001	19.67

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.9406
f_angle_d	0.5778
f_chiral_restr	0.0418
f_plane_restr	0.0037
f_bond_d	0.0023

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2336
Nucleic Acid Atoms
Solvent Atoms	381
Heterogen Atoms	36

Software

Software
Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing