7QLD | pdb_00007qld

Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I, Co-crystallization with HgCl2, Mutation Ser146Cys, (aa 32-198)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop and co-crystallization with 0.1 ul 2mM HgCl2

Crystal Properties
Matthews coefficient	Solvent content
3	59.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.36	α = 90
b = 85.36	β = 90
c = 191.965	γ = 120

Symmetry
Space Group	P 65 2 2

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-F		2018-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

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	2.15	48.38	99.9	0.041	0.045	0.018	0.999	25	10.4		23300

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	2.15	2.22			0.859	0.947	0.395	0.891		10.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	2.153	48.38	23231	1153	99.91	0.221	0.2189	0.22	0.2663	0.27	65.442

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]
1.531	0.765		1.531		-4.966

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.53
r_dihedral_angle_other_3_deg	18.248
r_dihedral_angle_3_deg	14.962
r_lrange_other	10.921
r_lrange_it	10.914
r_scangle_it	8.866
r_scangle_other	8.863
r_mcangle_it	7.462
r_mcangle_other	7.461
r_dihedral_angle_1_deg	6.662
r_scbond_it	6.658
r_scbond_other	6.635
r_mcbond_it	5.602
r_mcbond_other	5.585
r_angle_refined_deg	1.591
r_angle_other_deg	1.329
r_symmetry_xyhbond_nbd_refined	0.3
r_nbd_refined	0.211
r_symmetry_nbd_other	0.171
r_xyhbond_nbd_refined	0.156
r_nbtor_refined	0.15
r_nbd_other	0.142
r_symmetry_nbd_refined	0.121
r_ncsr_local_group_1	0.12
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2232
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing
ARP/wARP	model building