8AZB

Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in the unliganded state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8AY0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Ligand free DppE was crystallised in a sitting drop formed by mixing 150 nl of the unliganded protein at 9 mg.ml-1 with 150 nl of 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500.
Crystal Properties
Matthews coefficientSolvent content
2.2344.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.53α = 90
b = 91.08β = 90
c = 106.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
11.446.0999.60.0460.0530.0260.99920.97.4104801
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)
11.41.420.3440.4360.2620.8864.4

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-VALUE8AY01.446.089104711523299.4910.1820.18060.208416.093
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]
-0.239-0.3190.558
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.407
r_dihedral_angle_3_deg13.087
r_dihedral_angle_1_deg6.4
r_dihedral_angle_2_deg5.791
r_lrange_it5.46
r_lrange_other5.279
r_scangle_it4.219
r_scangle_other4.218
r_scbond_it2.888
r_scbond_other2.883
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.407
r_dihedral_angle_3_deg13.087
r_dihedral_angle_1_deg6.4
r_dihedral_angle_2_deg5.791
r_lrange_it5.46
r_lrange_other5.279
r_scangle_it4.219
r_scangle_other4.218
r_scbond_it2.888
r_scbond_other2.883
r_mcangle_other2.425
r_mcangle_it2.423
r_angle_refined_deg1.81
r_mcbond_it1.657
r_mcbond_other1.655
r_angle_other_deg0.593
r_symmetry_xyhbond_nbd_refined0.34
r_symmetry_nbd_refined0.243
r_nbd_refined0.231
r_symmetry_nbd_other0.189
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.183
r_nbd_other0.168
r_chiral_restr0.089
r_symmetry_nbtor_other0.079
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4029
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms

Software

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