7QFJ | pdb_00007qfj

Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain II (aa 194-362)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	RoseTTAFold		RoseTTAfold ab initio prediction

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293.15	Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Midas screen condition 50 (0.1M Tris, 50% v/v Pentaerythritol propoxylate (5/4 PO/OH)) with protein end concentration of 5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop, co-crystallization with 0.1 ul 2mM HgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.679	α = 90
b = 143.016	β = 96.699
c = 73.441	γ = 90

Symmetry
Space Group	P 1 21 1

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		2020-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.94290	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.5	48.63	99.9	0.084	0.1	0.053	0.998	17.1	6.8		46501

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59			0.6	0.715	0.384	0.866		6.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	RoseTTAfold ab initio prediction	2.5	46.028	46471	2290	99.927	0.207	0.2056	0.2	0.2425	0.24	RANDOM	47.942

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]
-4.037		0.827	3.417		0.415

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.171
r_dihedral_angle_3_deg	14.395
r_dihedral_angle_4_deg	11.204
r_lrange_it	9.706
r_scangle_it	7.354
r_mcangle_it	6.578
r_dihedral_angle_1_deg	6.48
r_scbond_it	5.063
r_mcbond_it	4.336
r_angle_refined_deg	1.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.171
r_dihedral_angle_3_deg	14.395
r_dihedral_angle_4_deg	11.204
r_lrange_it	9.706
r_scangle_it	7.354
r_mcangle_it	6.578
r_dihedral_angle_1_deg	6.48
r_scbond_it	5.063
r_mcbond_it	4.336
r_angle_refined_deg	1.336
r_symmetry_nbd_refined	0.317
r_nbtor_refined	0.288
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.089
r_gen_planes_refined	0.008
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7788
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

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 R01GM157729.