7PJ6

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PJ3

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
2.21	44.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.291	α = 90
b = 92.543	β = 90
c = 124.795	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	0.979260	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	1.3	46.27	99.9	0.065	0.019	19.6	13		67551

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	1.3	1.32			0.765	0.222

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7PJ3	1.3	46.254	67509	3387	99.883	0.15	0.1491	0.15	0.1745	0.18	20.59

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]
1.142			-0.845		-0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.965
r_dihedral_angle_4_deg	22.02
r_dihedral_angle_3_deg	11.791
r_dihedral_angle_1_deg	6.365
r_rigid_bond_restr	3.492
r_scangle_it	3.224
r_scangle_other	3.223
r_lrange_it	3.207
r_lrange_other	3.151
r_scbond_other	2.721
r_scbond_it	2.72
r_mcangle_other	1.974
r_mcangle_it	1.973
r_angle_refined_deg	1.677
r_angle_other_deg	1.626
r_mcbond_it	1.6
r_mcbond_other	1.592
r_nbd_other	0.246
r_symmetry_nbd_refined	0.233
r_nbd_refined	0.221
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.171
r_metal_ion_refined	0.163
r_symmetry_metal_ion_refined	0.149
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.01
r_bond_other_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	115

Software

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