8OJW

Streptavidin WT artificial metalloenzyme for carboamination


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PK2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42982.0 M ammonium sulfate 0.1 M sodium acetate -> soaking experiment by pH adjustment to pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.3447.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.82α = 90
b = 57.82β = 90
c = 184.462γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000305674358714SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.4846.15899.90.1170.1230.0380.99814.219.326459
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.511.5891.7160.6370.61213.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.48446.15826428135499.8980.1810.17950.202122.298
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]
-0.052-0.0520.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg13.856
r_dihedral_angle_3_deg12.315
r_dihedral_angle_2_deg8.909
r_lrange_it8.604
r_lrange_other7.94
r_dihedral_angle_1_deg7.515
r_scangle_it4.952
r_scangle_other3.967
r_scbond_it3.353
r_mcangle_it3.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg13.856
r_dihedral_angle_3_deg12.315
r_dihedral_angle_2_deg8.909
r_lrange_it8.604
r_lrange_other7.94
r_dihedral_angle_1_deg7.515
r_scangle_it4.952
r_scangle_other3.967
r_scbond_it3.353
r_mcangle_it3.324
r_mcangle_other3.323
r_scbond_other2.748
r_mcbond_it2.281
r_mcbond_other2.258
r_angle_refined_deg2.004
r_angle_other_deg0.684
r_xyhbond_nbd_refined0.229
r_symmetry_nbd_other0.202
r_nbd_refined0.194
r_nbtor_refined0.189
r_nbd_other0.177
r_symmetry_xyhbond_nbd_refined0.142
r_symmetry_xyhbond_nbd_other0.113
r_chiral_restr0.102
r_symmetry_nbd_refined0.092
r_symmetry_nbtor_other0.09
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms920
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing