Experiment: 9CGY

Structure of the Pel modification enzyme PelA from Pseudomonas thermotolerans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.17 M ammonium sulfate, 0.085 M sodium citrate pH 5.6, 25.5% (w/v) PEG4000, and 15% (v/v) glycerol (TOP96 condition #A10)

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.631	α = 90
b = 93.582	β = 90
c = 124.104	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 EIGER X 9M		2021-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.979338	NSLS-II	17-ID-1

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	2.09	29.66	99.8	0.0489	13.72	1.9		107145			29.65

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	2.09	2.17	98.54		0.2217		1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	2.09	29.66	1.35	107145	3806	99.46	0.1833	0.1817	0.1821	0.2264	0.2259	33.3

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	6.0045
f_angle_d	1.0919
f_chiral_restr	0.058
f_plane_restr	0.0111
f_bond_d	0.0107

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6359
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XPREP	data reduction
XDS	data scaling
SHELXDE	phasing