7PJ4 | pdb_00007pj4

Crystal structure of catalytic domain in closed conformation of LytB (E585Q)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	7PJ3

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.651	α = 90
b = 92.679	β = 90
c = 124.196	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	1.25	46.34	100	0.066	0.02	20.4	12		74735			12.1

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	1.25	1.27			0.763	0.226

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	1.25	43.454	74683	3754	99.973	0.137	0.136	0.14	0.1623	0.16	14.818

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]
0.953			-0.439		-0.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.228
r_dihedral_angle_4_deg	18.901
r_dihedral_angle_3_deg	10.828
r_rigid_bond_restr	6.124
r_dihedral_angle_1_deg	6.033
r_lrange_it	3.003
r_scangle_it	2.853
r_scangle_other	2.852
r_lrange_other	2.798
r_scbond_it	2.423
r_scbond_other	2.422
r_angle_other_deg	1.765
r_angle_refined_deg	1.63
r_mcangle_other	1.514
r_mcangle_it	1.512
r_mcbond_it	1.2
r_mcbond_other	1.178
r_nbd_refined	0.222
r_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.202
r_symmetry_nbd_other	0.197
r_symmetry_nbd_refined	0.195
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.16
r_metal_ion_refined	0.15
r_symmetry_metal_ion_refined	0.15
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.018
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	38

Software

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