4JXC

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CIW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298100 mM Tris, 200 mM Li2SO4, 30% PEG 4000, Anaerobic chamber (N2/H2 95/5%) , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.132α = 90
b = 78.729β = 90
c = 86.209γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-06-21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.456085.4119182101819
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5488.06

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3CIW1.558.125235652356280998.140.123630.123630.12140.16553RANDOM10.767
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]
0.5-0.09-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.576
r_dihedral_angle_4_deg15.341
r_dihedral_angle_1_deg11.831
r_dihedral_angle_3_deg11.722
r_sphericity_free10.043
r_scangle_it4.028
r_sphericity_bonded3.847
r_mcangle_it3.107
r_scbond_it2.956
r_mcbond_it2.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.576
r_dihedral_angle_4_deg15.341
r_dihedral_angle_1_deg11.831
r_dihedral_angle_3_deg11.722
r_sphericity_free10.043
r_scangle_it4.028
r_sphericity_bonded3.847
r_mcangle_it3.107
r_scbond_it2.956
r_mcbond_it2.357
r_rigid_bond_restr1.826
r_angle_refined_deg1.74
r_mcbond_other1.197
r_angle_other_deg1.01
r_chiral_restr0.112
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2726
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms206

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling