8WOK

Crystal structure of PL7 family alginate lyase AlyMc

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	2.5 M Ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.44	α = 90
b = 65.013	β = 95.073
c = 82.182	γ = 90

Symmetry
Space Group	P 1 21 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	Bruker PHOTON III		2022-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.34

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	23.99	99.3	0.979	10.6	5.4		36355

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.595

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	20.149	36317	1789	99.151	0.173	0.1707	0.2147	19.648

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]
0.277		-0.265	-0.734		0.496

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.344
r_dihedral_angle_3_deg	14.406
r_dihedral_angle_1_deg	7.724
r_dihedral_angle_2_deg	6.198
r_lrange_it	5.138
r_scangle_it	3.854
r_scbond_it	2.929
r_mcangle_it	2.672
r_mcbond_it	2.046
r_angle_refined_deg	2.031
r_nbtor_refined	0.308
r_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.195
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.16
r_chiral_restr	0.136
r_bond_refined_d	0.015
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4215
Nucleic Acid Atoms
Solvent Atoms	560
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
XDS	data reduction