8B2F

SH3-like cell wall binding domain of the GH24 family muramidase from Trichophaea saccata in complex with triglycine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8B2S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	10 mM triglycine added to the protein prior to crystallisation. Morpheus screen, condition D10

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.105	α = 76.679
b = 27.234	β = 81.267
c = 50.039	γ = 72.662

Symmetry
Space Group	P 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	DECTRIS EIGER2 XE 16M		2022-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.18	48.5	67	0.021	0.029	0.021	0.999	28.1	3.4		27938

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.18	1.2	4.7		0.145	0.206	0.145	0.977	3	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8B2S	1.183	48.497	27928	1391	67.044	0.115	0.1131	0.11	0.146	0.15	12.994

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]
-0.602	-0.013	-0.325	-0.094	-0.153	0.524

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.519
r_dihedral_angle_3_deg	9.331
r_dihedral_angle_1_deg	5.716
r_lrange_it	3.36
r_rigid_bond_restr	3.239
r_dihedral_angle_2_deg	2.966
r_lrange_other	2.933
r_scangle_it	2.737
r_scangle_other	2.735
r_scbond_other	2.508
r_scbond_it	2.492
r_mcangle_it	2.368
r_mcangle_other	2.366
r_mcbond_it	1.72
r_mcbond_other	1.72
r_angle_refined_deg	1.396
r_angle_other_deg	0.498
r_xyhbond_nbd_refined	0.318
r_nbd_refined	0.222
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.179
r_nbd_other	0.169
r_symmetry_nbd_refined	0.147
r_ncsr_local_group_1	0.092
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.07
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1120
Nucleic Acid Atoms	26
Solvent Atoms	138
Heterogen Atoms	17

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement