7PL3

Crystal structure of catalytic domain in closed conformation of LytB from Streptococcus pneumoniae

X-RAY DIFFRACTION

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	44.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.157	α = 90
b = 92.675	β = 90
c = 124.56	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		2019-11-08	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	1.78	43.43	99.7	0.093	0.042	11.5	5.6		26519			19.58

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	1.78	1.82			0.763	0.354

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4Q2W	1.8	43.43	24271	1354	99.56	0.1596	0.157	0.2072	RANDOM	24.393

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]
2.44			-1.76		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.127
r_dihedral_angle_4_deg	25.556
r_dihedral_angle_3_deg	13.148
r_dihedral_angle_1_deg	6.34
r_rigid_bond_restr	4.393
r_angle_refined_deg	1.788
r_angle_other_deg	1.473
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.127
r_dihedral_angle_4_deg	25.556
r_dihedral_angle_3_deg	13.148
r_dihedral_angle_1_deg	6.34
r_rigid_bond_restr	4.393
r_angle_refined_deg	1.788
r_angle_other_deg	1.473
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	31

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.