7NE7

oligopeptidase B from S. proteomaculans with modified hinge region in complex with N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TF5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277200 mM Lithium sulfate, 100 mM Bis-Tris pH 5.5, 23% PEG 3350, TCK
Crystal Properties
Matthews coefficientSolvent content
2.5752.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.32α = 90
b = 101.1β = 90
c = 108.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252019-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.8KURCHATOV SNCK4.4

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
12.319.9899.710.0577.987.9235505
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)
12.32.3699.010.242.146.14

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 REPLACEMENTTHROUGHOUT6TF52.319.9834680182599.710.19060.18840.2337RANDOM27.198
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]
-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.298
r_dihedral_angle_4_deg18.073
r_dihedral_angle_3_deg17.584
r_dihedral_angle_1_deg7.704
r_angle_refined_deg1.645
r_angle_other_deg1.261
r_chiral_restr0.102
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.298
r_dihedral_angle_4_deg18.073
r_dihedral_angle_3_deg17.584
r_dihedral_angle_1_deg7.704
r_angle_refined_deg1.645
r_angle_other_deg1.261
r_chiral_restr0.102
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5545
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing