5XN3

Crystal structure of SPSB2 in complex with a rational designed RGD containing cyclic peptide inhibitor of SPSB2-iNOS interaction


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72880.2M ammonium tartrate dibasic, pH 7.0, 20% (w/v) polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.0539.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.49α = 90
b = 64.6β = 102.95
c = 47.59γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9778SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.3464.691.20.06213.34.538904
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.3690.20.692.24.3

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 REPLACEMENTTHROUGHOUT3EMW1.3446.3836938193390.310.180950.179920.20009RANDOM15.064
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]
-0.250.31-0.730.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.372
r_dihedral_angle_3_deg12.415
r_dihedral_angle_4_deg10.835
r_dihedral_angle_1_deg6.47
r_long_range_B_other4.712
r_long_range_B_refined4.711
r_scangle_other4.096
r_scbond_it2.734
r_scbond_other2.732
r_angle_refined_deg2.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.372
r_dihedral_angle_3_deg12.415
r_dihedral_angle_4_deg10.835
r_dihedral_angle_1_deg6.47
r_long_range_B_other4.712
r_long_range_B_refined4.711
r_scangle_other4.096
r_scbond_it2.734
r_scbond_other2.732
r_angle_refined_deg2.253
r_mcangle_it2.203
r_mcangle_other2.203
r_mcbond_it1.496
r_mcbond_other1.492
r_angle_other_deg1.136
r_chiral_restr0.136
r_bond_refined_d0.024
r_gen_planes_refined0.013
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 Atoms1567
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing