7QFL | pdb_00007qfl

Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain II (aa 199-308)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QEC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	protein stock solution of 18.5 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 1-1 (0.18 M lithium sulfate, 90 mM sodium acetate pH 4.5 and 45 % w/v PEG 400) with protein end concentration of 12.3 mg/mL corresponding to 66.67 % of protein solution in the 1.5 uL drop.

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.851	α = 90
b = 55.851	β = 90
c = 63.732	γ = 120

Symmetry
Space Group	P 31 2 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-F		2017-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.4	48.37	100	0.085	0.095	0.042	0.997	13.6	9.5		23163

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	1.4	1.42			0.85	0.953	0.427	0.821		9.1

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	7QEC	1.4	48.368	23133	1177	99.97	0.172	0.1702	0.18	0.1981	0.2	19.088

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]
-0.361	-0.181		-0.361		1.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.481
r_dihedral_angle_4_deg	18.184
r_dihedral_angle_3_deg	10.405
r_dihedral_angle_1_deg	6.325
r_lrange_it	5.608
r_lrange_other	5.468
r_scangle_it	5.008
r_scangle_other	5.004
r_scbond_it	3.554
r_scbond_other	3.554
r_mcangle_other	2.472
r_mcangle_it	2.468
r_angle_refined_deg	2.032
r_mcbond_it	1.725
r_mcbond_other	1.643
r_angle_other_deg	1.547
r_symmetry_nbd_refined	0.273
r_nbd_other	0.237
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.142
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	765
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	9

Software

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