2GOJ

The crystal structure of the enzyme Fe-superoxide dismutase from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ISAPDB ENTRY 1ISA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529125.5% PEG 4000 (w/v), 0.17 M Sodium Acetate, 0.085 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1241.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.402α = 90
b = 78.417β = 90
c = 88.369γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIC2002-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
1231.6295.30.0987.56.42513122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1173.30.3722.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ISA231.6222405724057126694.970.157690.155760.19389RANDOM14.498
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.576
r_scangle_it2.525
r_scbond_it1.558
r_angle_refined_deg1.107
r_mcangle_it1.053
r_angle_other_deg0.796
r_mcbond_it0.55
r_symmetry_vdw_other0.273
r_nbd_other0.232
r_symmetry_hbond_refined0.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.576
r_scangle_it2.525
r_scbond_it1.558
r_angle_refined_deg1.107
r_mcangle_it1.053
r_angle_other_deg0.796
r_mcbond_it0.55
r_symmetry_vdw_other0.273
r_nbd_other0.232
r_symmetry_hbond_refined0.216
r_nbd_refined0.195
r_xyhbond_nbd_refined0.143
r_symmetry_vdw_refined0.135
r_nbtor_other0.084
r_chiral_restr0.072
r_metal_ion_refined0.04
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3175
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement