8ONO

Modified oligopeptidase B from S. proteamaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OB1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277200 mM Lithium sulfate, 100 mM Bis-Tris pH 5.5, 23% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5551.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.09α = 90
b = 100.62β = 90
c = 108.63γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.8SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.653098.570.050.0569.26335.8495311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.740.330.3592.29

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6529.5990588467398.350.187780.186110.2198RANDOM23.035
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.236
r_dihedral_angle_4_deg19.797
r_dihedral_angle_3_deg14.798
r_dihedral_angle_1_deg7.579
r_long_range_B_refined6.359
r_long_range_B_other6.325
r_scangle_other4.606
r_mcangle_it3.28
r_mcangle_other3.28
r_scbond_it3.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.236
r_dihedral_angle_4_deg19.797
r_dihedral_angle_3_deg14.798
r_dihedral_angle_1_deg7.579
r_long_range_B_refined6.359
r_long_range_B_other6.325
r_scangle_other4.606
r_mcangle_it3.28
r_mcangle_other3.28
r_scbond_it3.088
r_scbond_other3.088
r_mcbond_it2.234
r_mcbond_other2.232
r_angle_refined_deg1.795
r_angle_other_deg1.458
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5545
Nucleic Acid Atoms
Solvent Atoms536
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing