Experiment: 7WXQ

Crystal Structure of PL-5 family polysaccharide lyase PanPL-H172A mutant from Pandoraea apista in apo form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295.15	0.1 M Sodium acetate trihydrate pH 5.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.918	α = 90
b = 84.251	β = 90
c = 91.78	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	CMOS	BRUKER PHOTON 100	Helios-MX-Cu	2019-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.03	62.07	97.8	0.0963	0.998	18.57	13.25		18270			13

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.13	92.7		0.2778	0.946	4.38	5.06

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	7WXJ	2.03	62.07	1.34	18147	847	97.39	0.1934	0.1911	0.1916	0.2396	0.2388	13.81

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	4.3007
f_angle_d	0.5931
f_chiral_restr	0.0404
f_plane_restr	0.0049
f_bond_d	0.0036

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2405
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing