6GMI

Genetic Engineering of an Artificial Metalloenzyme for Transfer Hydrogenation of a Self-Immolative Substrate in E. coli's Periplasm.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QCB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1 M SPG 9 pH (Buffer) 25 %w/v PEG 1500 (Precipitant)
Crystal Properties
Matthews coefficientSolvent content
2.0439.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.507α = 90
b = 57.507β = 90
c = 184.13γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

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
11.646.071000.11715.625.420991
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)
11.61.634.33

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 REPLACEMENTTHROUGHOUT2qcb1.646.0719899106599.980.187280.186610.1994RANDOM30.467
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]
-0.37-0.370.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.836
r_dihedral_angle_4_deg20.461
r_dihedral_angle_3_deg12.887
r_long_range_B_refined8.227
r_long_range_B_other8.227
r_dihedral_angle_1_deg7.145
r_scangle_other5.26
r_mcangle_it4.062
r_mcangle_other4.059
r_scbond_it3.574
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.836
r_dihedral_angle_4_deg20.461
r_dihedral_angle_3_deg12.887
r_long_range_B_refined8.227
r_long_range_B_other8.227
r_dihedral_angle_1_deg7.145
r_scangle_other5.26
r_mcangle_it4.062
r_mcangle_other4.059
r_scbond_it3.574
r_scbond_other3.533
r_mcbond_it3.012
r_mcbond_other2.926
r_angle_refined_deg2.523
r_angle_other_deg1.04
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms896
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing