2WLB

Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyces pombe mitochondria


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4277VAPOUR DIFFUSION, SITTING DROP, 4 DEGR. CENTIGRADE. RESERVOIR: 0.04M HEPES,1.8M NA-CITRATE, 3% GLYCEROL,PH7.0. PROTEIN SOLUTION: 18.4MG/ML PROTEIN, 20MM POTASSIUMPHOSPHATE,PH7.4. 0.3 PLUS 0.3 MICROLITER DROPLET.
Crystal Properties
Matthews coefficientSolvent content
2.8356.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.965α = 90
b = 81.965β = 90
c = 68.289γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray278IMAGE PLATEMAR scanner 345 mm plate2004-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU H2B

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
12.62099.50.118.53.4800656.1
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)
12.62.7892.40.513.43.5

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 REPLACEMENTTHROUGHOUTPDB ENTRIES 1E6E,1AYF,1L6V,2BT62.620800639099.50.1840.1820.235RANDOM45.15
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]
0.310.160.31-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.132
r_dihedral_angle_3_deg18.903
r_dihedral_angle_4_deg13.795
r_scangle_it9.292
r_scbond_it6.76
r_dihedral_angle_1_deg5.593
r_mcangle_it3.93
r_mcbond_it3.23
r_angle_refined_deg1.453
r_angle_other_deg0.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.132
r_dihedral_angle_3_deg18.903
r_dihedral_angle_4_deg13.795
r_scangle_it9.292
r_scbond_it6.76
r_dihedral_angle_1_deg5.593
r_mcangle_it3.93
r_mcbond_it3.23
r_angle_refined_deg1.453
r_angle_other_deg0.915
r_symmetry_vdw_other0.31
r_nbd_refined0.215
r_nbd_other0.202
r_symmetry_vdw_refined0.2
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.147
r_nbtor_other0.09
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1567
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SWISS-MODELLERphasing
PHASERphasing
REFMACrefinement