8RHE

Lytic Transglycosylase MltD of Pseudomonas aeruginosa bound to the Natural Product Bulgecin A

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, HANGING DROP	6.5	291	0.1 M MES pH 6.5, 25% w/v PEG 550 MME, and 10 mM zinc sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.224	α = 90
b = 113.408	β = 90
c = 116.858	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 PILATUS 6M		2022-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

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	1.95	42.18	89.8	0.999	11.4	6		49604

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	1.95	1.99			0.4712	1.264

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	1.95	42.18	44670	2194	99.81	0.192	0.1905	0.213	44.818

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]
-0.086			0.202		-0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.292
r_dihedral_angle_3_deg	15.123
r_lrange_it	6.817
r_lrange_other	6.785
r_dihedral_angle_2_deg	6.381
r_dihedral_angle_1_deg	5.687
r_scangle_it	4.133
r_scangle_other	4.133
r_mcangle_it	3.274
r_mcangle_other	3.273
r_scbond_it	2.456
r_scbond_other	2.453
r_mcbond_it	2.013
r_mcbond_other	2.012
r_dihedral_angle_other_2_deg	1.866
r_angle_refined_deg	1.051
r_angle_other_deg	0.359
r_symmetry_nbd_refined	0.216
r_nbd_refined	0.215
r_nbd_other	0.197
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.135
r_ncsr_local_group_1	0.128
r_metal_ion_refined	0.118
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4457
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing