8ARN

Crystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with an endogenous tetrapeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RKM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291Crystals of OppA were obtained from hanging drops composed of 2 microlitres of reservoir solution consisting of 0.1 M MMT, 22.5% PEG 1500 and 2.5% DMSO pH 8.0 and 2 microlitres protein at 18 mg.ml-1 with crystal optimisation following a seeding protocol.
Crystal Properties
Matthews coefficientSolvent content
2.1141.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.52α = 90
b = 65.89β = 100.97
c = 153.29γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.82DiamondI03

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
11.555.02599.90.0450.0590.0380.99812.64.2158694
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)
11.51.530.7230.9550.6170.6094.2

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-VALUE1RKM1.555.025158693784999.8610.1790.17720.206622.694
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]
-0.661-0.2831.266-0.461
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.093
r_dihedral_angle_6_deg16.002
r_lrange_other15.461
r_dihedral_angle_3_deg13.791
r_dihedral_angle_2_deg7.4
r_dihedral_angle_1_deg6.494
r_scangle_it4.666
r_scangle_other4.666
r_scbond_it3.151
r_scbond_other3.151
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.093
r_dihedral_angle_6_deg16.002
r_lrange_other15.461
r_dihedral_angle_3_deg13.791
r_dihedral_angle_2_deg7.4
r_dihedral_angle_1_deg6.494
r_scangle_it4.666
r_scangle_other4.666
r_scbond_it3.151
r_scbond_other3.151
r_mcangle_it2.561
r_mcangle_other2.561
r_mcbond_it1.975
r_mcbond_other1.974
r_angle_refined_deg1.614
r_angle_other_deg0.557
r_symmetry_nbd_refined0.234
r_nbd_refined0.221
r_symmetry_nbd_other0.193
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.182
r_nbd_other0.178
r_symmetry_xyhbond_nbd_refined0.177
r_chiral_restr0.084
r_symmetry_nbtor_other0.08
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_xyhbond_nbd_other0.008
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8171
Nucleic Acid Atoms
Solvent Atoms884
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
DIALSdata reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing