7QFL

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7QEC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15protein 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 coefficientSolvent content
2.4850.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.851α = 90
b = 55.851β = 90
c = 63.732γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.448.371000.0850.0950.0420.99713.69.523163
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)RedundancyNumber Unique Reflections (All)
11.41.420.850.9530.4270.8219.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7QEC1.448.36823133117799.970.1720.17020.198119.088
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]
-0.361-0.181-0.3611.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.481
r_dihedral_angle_4_deg18.184
r_dihedral_angle_3_deg10.405
r_dihedral_angle_1_deg6.325
r_lrange_it5.608
r_lrange_other5.468
r_scangle_it5.008
r_scangle_other5.004
r_scbond_it3.554
r_scbond_other3.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.481
r_dihedral_angle_4_deg18.184
r_dihedral_angle_3_deg10.405
r_dihedral_angle_1_deg6.325
r_lrange_it5.608
r_lrange_other5.468
r_scangle_it5.008
r_scangle_other5.004
r_scbond_it3.554
r_scbond_other3.554
r_mcangle_other2.472
r_mcangle_it2.468
r_angle_refined_deg2.032
r_mcbond_it1.725
r_mcbond_other1.643
r_angle_other_deg1.547
r_symmetry_nbd_refined0.273
r_nbd_other0.237
r_nbd_refined0.208
r_xyhbond_nbd_refined0.19
r_symmetry_nbd_other0.174
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_refined0.142
r_chiral_restr0.09
r_symmetry_nbtor_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms765
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building