4Y04

Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis (Space)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION293tri-potassium citrate, PEG 8000 Crystallisation under micro gravity at ISS Kibo.
Crystal Properties
Matthews coefficientSolvent content
2.7955.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.14α = 90
b = 103.28β = 90
c = 175.31γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702014-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.664099.60.0519.86.2105914
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.798.92.55.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4Y011.6640100599526699.90.188070.186130.22473RANDOM32.641
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]
-1.78-1.12.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.089
r_dihedral_angle_4_deg18.735
r_dihedral_angle_3_deg14.047
r_dihedral_angle_1_deg7.453
r_long_range_B_refined6.892
r_long_range_B_other6.712
r_scangle_other5.473
r_scbond_it3.831
r_scbond_other3.83
r_mcangle_other3.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.089
r_dihedral_angle_4_deg18.735
r_dihedral_angle_3_deg14.047
r_dihedral_angle_1_deg7.453
r_long_range_B_refined6.892
r_long_range_B_other6.712
r_scangle_other5.473
r_scbond_it3.831
r_scbond_other3.83
r_mcangle_other3.618
r_mcangle_it3.617
r_mcbond_it2.768
r_mcbond_other2.767
r_angle_refined_deg1.955
r_angle_other_deg1.126
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5522
Nucleic Acid Atoms
Solvent Atoms696
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction