7QFG
Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain III (aa 309-444)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 7QEH |
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; Index screen condition A9 (0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.04 | 59.51 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 100.628 | α = 90 |
b = 43.943 | β = 98.824 |
c = 42.488 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 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 EIGER2 X 16M | 2019-03-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.25430 | 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 | 1.65 | 41.99 | 99.4 | 0.074 | 0.102 | 0.07 | 0.985 | 11.3 | 3.2 | 22102 |
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 | 1.65 | 1.68 | 0.15 | 0.206 | 0.141 | 0.951 | 3 |
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 | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7QEH | 1.65 | 41.99 | 22101 | 1143 | 99.321 | 0.16 | 0.1585 | 0.1836 | 16.567 |
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] | |
0.134 | -0.092 | 0.609 | -0.682 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.61 |
r_dihedral_angle_3_deg | 11.856 |
r_dihedral_angle_4_deg | 9.205 |
r_dihedral_angle_1_deg | 7.026 |
r_lrange_it | 5.84 |
r_lrange_other | 5.608 |
r_scangle_it | 4.855 |
r_scangle_other | 4.852 |
r_scbond_it | 3.119 |
r_scbond_other | 3.116 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1081 |
Nucleic Acid Atoms | |
Solvent Atoms | 197 |
Heterogen Atoms | 18 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |