8YXK

X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	20% (w/v) PEG 3350, 200mM sodium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.43	α = 90
b = 80.47	β = 104.117
c = 48.77	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	IMAGE PLATE	RIGAKU RAXIS VII		2021-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.87	19.322	98.5	0.996	9	3.7		29563

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	1.87	1.92			0.761

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	1.87	19.322	29563	1501	98.497	0.249	0.2472	0.2868	21.628

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]
-0.133		0.029	0.036		0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.546
r_dihedral_angle_3_deg	17.998
r_dihedral_angle_1_deg	7.549
r_dihedral_angle_4_deg	6.096
r_lrange_it	5.317
r_lrange_other	5.314
r_scangle_it	4.231
r_scangle_other	4.23
r_mcangle_other	2.909
r_mcangle_it	2.908
r_scbond_it	2.783
r_scbond_other	2.783
r_mcbond_it	2.061
r_mcbond_other	2.054
r_angle_other_deg	1.245
r_angle_refined_deg	1.186
r_nbd_refined	0.205
r_symmetry_nbd_other	0.2
r_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.148
r_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.054
r_gen_planes_refined	0.014
r_bond_refined_d	0.005
r_gen_planes_other	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing