4ZAF

Structure of UbiX in complex with oxidised FMN and dimethylallyl monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherThis structure was solved using difference fourier

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29712% PEG 3350, 150mM sodium thiocyanate, and 100mM Tris pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.6653.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.9α = 90
b = 141.9β = 90
c = 141.9γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

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
11.7170.951000.02718.76.724314
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)
1.711.751000.2982.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTThis structure was solved using difference fourier1.7170.9524314129599.920.13920.137440.17231RANDOM23.416
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_deg38.353
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg11.893
r_long_range_B_refined6.489
r_long_range_B_other6.488
r_dihedral_angle_1_deg6.202
r_scangle_other5.161
r_scbond_it3.472
r_scbond_other3.461
r_mcangle_it3.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.353
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg11.893
r_long_range_B_refined6.489
r_long_range_B_other6.488
r_dihedral_angle_1_deg6.202
r_scangle_other5.161
r_scbond_it3.472
r_scbond_other3.461
r_mcangle_it3.054
r_mcangle_other3.053
r_mcbond_it2.257
r_mcbond_other2.256
r_angle_refined_deg2.119
r_angle_other_deg0.996
r_chiral_restr0.285
r_bond_refined_d0.025
r_gen_planes_refined0.016
r_bond_other_d0.002
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 Atoms139
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing