7ARS

The de novo designed hybrid alpha/beta-miniprotein (with Se-Methionine)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
othernot deposited

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52910.2 M magnesium chloride hexahydrate 0.1 M Tris pH 8.5 20 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.346.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.089α = 90
b = 35.481β = 111.24
c = 41.919γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.155097.60.050.9916.616.32471218.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.2288.50.430.912.955.6

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 REPLACEMENTTHROUGHOUTnot deposited1.1539.0723711100197.790.17630.17450.2202RANDOM20.083
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]
-0.090.32-2.341.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.387
r_dihedral_angle_4_deg22.652
r_dihedral_angle_3_deg12.71
r_rigid_bond_restr7.962
r_dihedral_angle_1_deg5.819
r_angle_refined_deg2.558
r_angle_other_deg1.569
r_chiral_restr0.148
r_bond_refined_d0.02
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.387
r_dihedral_angle_4_deg22.652
r_dihedral_angle_3_deg12.71
r_rigid_bond_restr7.962
r_dihedral_angle_1_deg5.819
r_angle_refined_deg2.558
r_angle_other_deg1.569
r_chiral_restr0.148
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms508
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction