7QFK | pdb_00007qfk

Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain II, Co-Crystallization with HgCl2, Mutation Ser316Cys (aa 194-362)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	RoseTTAFold		MR model calculated with RoseTTAFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; Index screen condition H12 (0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000) with protein end concentration of 5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.166	α = 90
b = 98.875	β = 90
c = 155.13	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 2M		2021-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.48	48.98	99.54	0.998	12.75	12.4		34927

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.484	2.573			0.836

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MR model calculated with RoseTTAFold	2.48	48.98	33175	1749	99.57	0.20312	0.20161	0.2067	0.23097	0.2357	RANDOM	47.694

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]
1.2			-2.49		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.759
r_dihedral_angle_4_deg	16.619
r_dihedral_angle_3_deg	13.763
r_dihedral_angle_1_deg	6.52
r_long_range_B_refined	5.888
r_long_range_B_other	5.873
r_scangle_other	3.593
r_mcangle_it	3.163
r_mcangle_other	3.163
r_scbond_it	2.317
r_scbond_other	2.298
r_mcbond_it	1.927
r_mcbond_other	1.927
r_angle_refined_deg	1.547
r_angle_other_deg	1.092
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5253
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	38

Software

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