7NE4

E125A 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
2.3547.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.84α = 90
b = 98.56β = 90
c = 108.26γ = 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
12.71744.999.920.0618.456.1820453
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)
12.7172.790.292.11

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 REPLACEMENTTHROUGHOUT6TF52.71744.8519430102399.920.25270.250.3056RANDOM28.828
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]
1.670.83-2.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.549
r_dihedral_angle_3_deg15.343
r_dihedral_angle_4_deg14.574
r_dihedral_angle_1_deg5.825
r_angle_refined_deg1.023
r_angle_other_deg0.904
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.549
r_dihedral_angle_3_deg15.343
r_dihedral_angle_4_deg14.574
r_dihedral_angle_1_deg5.825
r_angle_refined_deg1.023
r_angle_other_deg0.904
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5531
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing