7QVD

X-ray structure of the lytic transglycosylase SltB2 from Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	20% Polyethylene Glycol 4000, 0.1 M sodium acetate and 8% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.966	α = 90
b = 42.395	β = 95.646
c = 93.579	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	DECTRIS PILATUS 6M		2018-10-13	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)	R Merge I (Observed)	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	1.7	46.56	99	0.086	0.036	0.998	13	6.6		36814

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	99.3		1.072	0.435	0.698	2.3	6.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5ANZ	1.7	46.56	36801	1778	98.84	0.165	0.1639	0.1953	24.924

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]
0.505		1.45	-0.517		-0.269

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.849
r_dihedral_angle_4_deg	15.223
r_dihedral_angle_3_deg	13.221
r_dihedral_angle_1_deg	6.038
r_lrange_it	5.569
r_lrange_other	5.238
r_scangle_it	3.246
r_scangle_other	3.245
r_mcangle_it	2.187
r_mcangle_other	2.187
r_scbond_it	2
r_scbond_other	1.999
r_angle_refined_deg	1.467
r_angle_other_deg	1.453
r_mcbond_it	1.36
r_mcbond_other	1.352
r_xyhbond_nbd_other	0.315
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_other	0.214
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.189
r_symmetry_nbd_refined	0.186
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.167
r_metal_ion_refined	0.134
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2886
Nucleic Acid Atoms
Solvent Atoms	399
Heterogen Atoms	1

Software

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