7POD

Crystal structure of catalytic domain of LytB (E585Q) from Streptococcus pneumoniae in complex with NAG-NAM-NAG-NAM tetrasaccharide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	PEG 300 Bis-Tris Calcium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.144	α = 90
b = 92.522	β = 90
c = 124.572	γ = 90

Symmetry
Space Group	C 2 2 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		2019-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.5	46.26	99.5	0.048	0.016	24	9.9		43792			18.52

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53			0.66	0.217

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	7PL3	1.5	46.254	43749	2221	99.344	0.147	0.145	0.1938	22.101

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]
2.451			-1.387		-1.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.736
r_dihedral_angle_4_deg	22.626
r_dihedral_angle_3_deg	12.2
r_dihedral_angle_1_deg	6.55
r_rigid_bond_restr	6.544
r_scangle_it	4.091
r_scangle_other	4.089
r_lrange_it	4.018
r_lrange_other	3.982
r_scbond_it	3.652
r_scbond_other	3.652
r_mcangle_other	2.542
r_mcangle_it	2.541
r_mcbond_it	2.179
r_mcbond_other	2.175
r_angle_refined_deg	1.748
r_angle_other_deg	1.73
r_nbd_other	0.283
r_symmetry_metal_ion_refined	0.241
r_symmetry_nbd_refined	0.217
r_nbd_refined	0.213
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.133
r_metal_ion_refined	0.131
r_symmetry_xyhbond_nbd_other	0.102
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.018
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	92

Software

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