4ZAY

Structure of UbiX E49Q in complex with a covalent adduct between dimethylallyl monophosphate and reduced FMN


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
2.6753.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.02α = 90
b = 142.02β = 90
c = 142.02γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-08-10MSINGLE 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
11.5432.581000.02120.36.733304
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)
1.541.581000.26636.7

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 REPLACEMENTTHROUGHOUT1.5432.5833304175699.920.146920.145360.17604RANDOM23.058
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_deg39.476
r_dihedral_angle_4_deg17.869
r_dihedral_angle_3_deg12.141
r_dihedral_angle_1_deg6.383
r_long_range_B_refined6.356
r_long_range_B_other6.355
r_scangle_other4.988
r_scbond_it3.425
r_scbond_other3.425
r_mcangle_it2.963
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.476
r_dihedral_angle_4_deg17.869
r_dihedral_angle_3_deg12.141
r_dihedral_angle_1_deg6.383
r_long_range_B_refined6.356
r_long_range_B_other6.355
r_scangle_other4.988
r_scbond_it3.425
r_scbond_other3.425
r_mcangle_it2.963
r_mcangle_other2.961
r_angle_refined_deg2.377
r_mcbond_it2.279
r_mcbond_other2.278
r_angle_other_deg1.116
r_chiral_restr0.438
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_gen_planes_other0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1546
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing