8ARE

Crystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with a PhrE-derived pentapeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOppA-SNSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4291Crystals of BsOppA in complex with Ser-Arg-Asn-Val-Thr where grown from the products of an isothermal titration calorimetry experiment. This recovered material was fed into a crystallisation screening experiment in MRC-Wilden 96 well plates. A single crystal of BsOppA-SRNVT was grown from 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, glycine) 25% (w/v) PEG 1500 pH 4.0,
Crystal Properties
Matthews coefficientSolvent content
2.0941.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.861α = 90
b = 63.689β = 114.352
c = 100.06γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.952.2631000.2330.3130.2060.9553.24.137997
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)
11.91.941.0561.4150.9330.7584

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-VALUEOppA-SNSS1.952.26337789181199.3720.2550.25180.308415.642
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]
1.48-1.0111.549-1.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.821
r_dihedral_angle_3_deg15.394
r_dihedral_angle_2_deg7.198
r_dihedral_angle_1_deg7.084
r_lrange_it3.171
r_lrange_other3.099
r_scangle_it2.079
r_scangle_other2.074
r_mcangle_it1.67
r_mcangle_other1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.821
r_dihedral_angle_3_deg15.394
r_dihedral_angle_2_deg7.198
r_dihedral_angle_1_deg7.084
r_lrange_it3.171
r_lrange_other3.099
r_scangle_it2.079
r_scangle_other2.074
r_mcangle_it1.67
r_mcangle_other1.67
r_angle_refined_deg1.391
r_scbond_it1.315
r_scbond_other1.301
r_mcbond_it1.056
r_mcbond_other1.056
r_angle_other_deg0.478
r_symmetry_nbd_refined0.257
r_nbd_refined0.218
r_nbd_other0.218
r_symmetry_nbd_other0.196
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.182
r_symmetry_xyhbond_nbd_refined0.169
r_symmetry_nbtor_other0.08
r_chiral_restr0.065
r_symmetry_xyhbond_nbd_other0.041
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4060
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
ELVESdata processing
XDSdata reduction
Aimlessdata scaling
MOLREPphasing