4ZAZ

Structure of UbiX Y169F in complex with a covalent adduct formed between reduced FMN and dimethylallyl monophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29712% PEG 3350, 150mM sodium thiocyanate, and 100mM Tris pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.26α = 90
b = 142.26β = 90
c = 142.26γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.4550.399.90.02815.75.540068
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.490.3562.45.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.4550.340068206699.820.104690.10260.14723RANDOM21.217
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.865
r_sphericity_free26.056
r_dihedral_angle_4_deg19.614
r_sphericity_bonded13.407
r_dihedral_angle_3_deg13.341
r_dihedral_angle_1_deg6.593
r_scangle_other5.928
r_scbond_it5.654
r_scbond_other5.598
r_rigid_bond_restr5.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.865
r_sphericity_free26.056
r_dihedral_angle_4_deg19.614
r_sphericity_bonded13.407
r_dihedral_angle_3_deg13.341
r_dihedral_angle_1_deg6.593
r_scangle_other5.928
r_scbond_it5.654
r_scbond_other5.598
r_rigid_bond_restr5.406
r_long_range_B_refined5.007
r_long_range_B_other5.006
r_mcangle_it3.208
r_mcangle_other3.208
r_mcbond_it2.871
r_mcbond_other2.87
r_angle_refined_deg2.228
r_angle_other_deg1.304
r_chiral_restr0.462
r_bond_refined_d0.025
r_gen_planes_refined0.014
r_gen_planes_other0.006
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1545
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing