7PJ5 | pdb_00007pj5

Crystal structure of catalytic domain of LytB from Streptococcus pneumoniae in complex with NAG-NAG-NAG-NAG tetrasaccharide

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	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.679	α = 90
b = 92.358	β = 90
c = 124.3	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	0.979260	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	1.55	46.18	100	0.058	0.017	24.5	12.8		40276

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	1.55	1.58			0.701	0.199

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	1.55	46.174	40235	1991	99.975	0.146	0.1436	0.16	0.1917	0.2	23.592

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]
1.171			-1.672		0.501

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.094
r_dihedral_angle_4_deg	23.472
r_dihedral_angle_3_deg	12.753
r_dihedral_angle_1_deg	6.598
r_rigid_bond_restr	5.724
r_scangle_it	4.184
r_scangle_other	4.183
r_lrange_it	4.17
r_lrange_other	4.102
r_scbond_it	3.661
r_scbond_other	3.66
r_mcangle_other	3.103
r_mcangle_it	3.1
r_mcbond_it	2.769
r_mcbond_other	2.741
r_angle_other_deg	1.931
r_angle_refined_deg	1.668
r_nbd_other	0.323
r_symmetry_nbd_refined	0.258
r_symmetry_metal_ion_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.208
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.152
r_metal_ion_refined	0.119
r_symmetry_xyhbond_nbd_other	0.111
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.082
r_bond_other_d	0.018
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	88

Software

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