1MY6 | pdb_00001my6

The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ISCFeSOD from E.coli, PDB entry 1isc

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.7293.15VAPOR DIFFUSION, HANGING DROP, 293.15K, 0.1M Sodium Cacodylate pH 6.7, 0.2M Magnesium Acetate Tetrahydrate, 20% PEG 6K
Crystal Properties
Matthews coefficientSolvent content
2.6152.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.749α = 90
b = 63.644β = 110.45
c = 74.709γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.100NSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.67094.50.0886.3516.1853851-315.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.64293.40.320.326.3514.285643

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTFeSOD from E.coli, PDB entry 1isc1.67053851289694.460.195770.193770.210.232080.25RANDOM15.669
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]
1.640.82-1.540.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.88
r_scangle_it3.693
r_sphericity_free3.671
r_scbond_it2.616
r_sphericity_bonded2.124
r_mcangle_it1.91
r_angle_refined_deg1.623
r_rigid_bond_restr1.522
r_mcbond_it1.312
r_angle_other_deg0.903
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.88
r_scangle_it3.693
r_sphericity_free3.671
r_scbond_it2.616
r_sphericity_bonded2.124
r_mcangle_it1.91
r_angle_refined_deg1.623
r_rigid_bond_restr1.522
r_mcbond_it1.312
r_angle_other_deg0.903
r_symmetry_vdw_other0.297
r_nbd_other0.247
r_nbd_refined0.231
r_xyhbond_nbd_refined0.213
r_symmetry_hbond_refined0.206
r_symmetry_vdw_refined0.177
r_chiral_restr0.107
r_nbtor_other0.087
r_bond_refined_d0.016
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3128
Nucleic Acid Atoms
Solvent Atoms565
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
EPMRphasing