5B48

2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B46 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529815% PEG3350, 0.1 M Tris-HCl, 0.1 M NaBr
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.15α = 90
b = 145.878β = 90
c = 170.094γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2005-12-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A0.9780Photon FactoryBL-5A

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
12.55099.20.058274.365171
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)
12.52.5993.70.3731.723.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5B462.536.4761283327498.920.214660.211210.27799RANDOM67.549
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.258
r_dihedral_angle_3_deg19.755
r_dihedral_angle_4_deg17.32
r_long_range_B_refined10.914
r_long_range_B_other10.914
r_scangle_other8.061
r_dihedral_angle_1_deg7.337
r_mcangle_it7.047
r_mcangle_other7.046
r_scbond_it5.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.258
r_dihedral_angle_3_deg19.755
r_dihedral_angle_4_deg17.32
r_long_range_B_refined10.914
r_long_range_B_other10.914
r_scangle_other8.061
r_dihedral_angle_1_deg7.337
r_mcangle_it7.047
r_mcangle_other7.046
r_scbond_it5.236
r_scbond_other5.236
r_mcbond_it4.75
r_mcbond_other4.75
r_angle_refined_deg1.762
r_angle_other_deg1.106
r_chiral_restr0.101
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.006
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 Atoms12972
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing