4JYF

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.641α = 90
b = 78.762β = 90
c = 86.088γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.456099.10.053117963116913
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5496.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4558.125849458494311999.750.134510.132840.16613RANDOM13.8
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]
1.33-0.31-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_1_deg18.333
r_dihedral_angle_4_deg15.221
r_dihedral_angle_3_deg11.787
r_sphericity_free5.425
r_scangle_it3.281
r_sphericity_bonded2.781
r_scbond_it2.457
r_mcangle_it1.735
r_rigid_bond_restr1.732
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_1_deg18.333
r_dihedral_angle_4_deg15.221
r_dihedral_angle_3_deg11.787
r_sphericity_free5.425
r_scangle_it3.281
r_sphericity_bonded2.781
r_scbond_it2.457
r_mcangle_it1.735
r_rigid_bond_restr1.732
r_angle_refined_deg1.723
r_angle_other_deg1.432
r_mcbond_it1.232
r_mcbond_other0.501
r_symmetry_vdw_other0.277
r_nbd_refined0.265
r_nbd_other0.209
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.18
r_symmetry_hbond_refined0.155
r_chiral_restr0.11
r_nbtor_other0.085
r_bond_refined_d0.013
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2729
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms196

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling