7PJ3 | pdb_00007pj3

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q2W

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	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.276	α = 90
b = 92.614	β = 90
c = 124.392	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	1.43	46.31	100	0.04	0.012	31	13.1		50892

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	1.43	1.45			0.775	0.219

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	4Q2W	1.43	43.434	50848	2535	99.994	0.146	0.1438	0.14	0.1852	0.19	22.694

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]
2.288			-1.56		-0.729

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.545
r_dihedral_angle_4_deg	17.141
r_dihedral_angle_3_deg	11.689
r_dihedral_angle_1_deg	6.498
r_rigid_bond_restr	6.45
r_scangle_it	4.027
r_scangle_other	4.026
r_lrange_it	3.987
r_lrange_other	3.897
r_scbond_it	3.421
r_scbond_other	3.42
r_mcangle_other	2.496
r_mcangle_it	2.492
r_mcbond_it	2.163
r_mcbond_other	2.073
r_angle_other_deg	1.727
r_angle_refined_deg	1.597
r_nbd_other	0.256
r_symmetry_xyhbond_nbd_refined	0.255
r_nbd_refined	0.215
r_symmetry_nbd_other	0.204
r_metal_ion_refined	0.203
r_symmetry_nbd_refined	0.196
r_symmetry_metal_ion_refined	0.193
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.124
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.018
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	41

Software

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