4ZAX

Structure of UbiX in complex with oxidised prenylated FMN (radical)


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
2.6553.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.79α = 90
b = 141.79β = 90
c = 141.79γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.98DiamondI02

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
11.6142.7599.90.02420.15.629027
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)
1.611.651000.3352.55.4

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 REPLACEMENTTHROUGHOUT1.6142.7529027154199.820.144930.14360.17095RANDOM22.876
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_deg40.011
r_dihedral_angle_4_deg19.711
r_dihedral_angle_3_deg13.027
r_long_range_B_refined6.498
r_long_range_B_other6.496
r_dihedral_angle_1_deg6.458
r_scangle_other5.306
r_scbond_it3.549
r_scbond_other3.538
r_mcangle_it3.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.011
r_dihedral_angle_4_deg19.711
r_dihedral_angle_3_deg13.027
r_long_range_B_refined6.498
r_long_range_B_other6.496
r_dihedral_angle_1_deg6.458
r_scangle_other5.306
r_scbond_it3.549
r_scbond_other3.538
r_mcangle_it3.244
r_mcangle_other3.243
r_angle_refined_deg2.431
r_mcbond_it2.319
r_mcbond_other2.311
r_angle_other_deg1.734
r_chiral_restr0.276
r_bond_refined_d0.026
r_gen_planes_refined0.016
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms127
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing