7NE5

catalytically non active S532A mutant of oligopeptidase B from S. proteomaculans with modified hinge region


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
Crystal Properties
Matthews coefficientSolvent content
2.4650.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.71α = 90
b = 100.4β = 90
c = 108.67γ = 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
11.8847.899.80.04910.157.2563282
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)
11.881.9399.780.312.094.31

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 REPLACEMENTTHROUGHOUT6TF51.8847.7960144313899.80.20940.20710.2524RANDOM29.393
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.773
r_dihedral_angle_4_deg20.878
r_dihedral_angle_3_deg16.173
r_dihedral_angle_1_deg7.75
r_angle_refined_deg1.634
r_angle_other_deg1.347
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.773
r_dihedral_angle_4_deg20.878
r_dihedral_angle_3_deg16.173
r_dihedral_angle_1_deg7.75
r_angle_refined_deg1.634
r_angle_other_deg1.347
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5534
Nucleic Acid Atoms
Solvent Atoms386
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing