8RHI | pdb_00008rhi

Lytic Transglycosylase MltD of Pseudomonas aeruginosa in a ternary complex bound to Bulgecin A and chito-tetraose

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
2.06	40.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.248	α = 90
b = 117.036	β = 90
c = 120.146	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		2022-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	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	1.98	83.84	87.8	0.9992	16.72	13.13		47136

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	1.98	2.03	96.2		0.6743	1.696

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.98	83.835	45208	2232	99.634	0.191	0.1902	0.2	0.2155	0.22	49.644

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]
1.081			-0.478		-0.603

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.908
r_dihedral_angle_3_deg	14.229
r_lrange_it	6.986
r_lrange_other	6.975
r_dihedral_angle_1_deg	5.778
r_dihedral_angle_2_deg	5.231
r_scangle_it	4.604
r_scangle_other	4.603
r_mcangle_it	3.717
r_mcangle_other	3.716
r_scbond_it	2.788
r_scbond_other	2.785
r_mcbond_it	2.248
r_mcbond_other	2.248
r_dihedral_angle_other_2_deg	2.188
r_angle_refined_deg	1.026
r_angle_other_deg	0.364
r_nbd_refined	0.216
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.159
r_nbd_other	0.159
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_nbd_refined	0.132
r_ncsr_local_group_1	0.119
r_metal_ion_refined	0.108
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.053
r_bond_refined_d	0.007
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	4423
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	165

Software

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