2GPC

The crystal structure of the enzyme Fe-superoxide dismutase from Trypanosoma cruzi


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829124% PEG4000, 0.2 M MgCl2, 0.1 M TRIS-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.626α = 90
b = 38.985β = 105.85
c = 91.073γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2002-02-25MSINGLE 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
11.929.594.60.06310.64.42712722
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)
1.91.9969.90.2762.72.9

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 REPLACEMENTTHROUGHOUT1ISA1.929.4922801226598141494.560.156660.154490.1981RANDOM14.471
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]
0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.694
r_scangle_it2.23
r_scbond_it1.366
r_angle_refined_deg1.118
r_mcangle_it0.877
r_angle_other_deg0.779
r_mcbond_it0.46
r_nbd_other0.228
r_symmetry_vdw_other0.201
r_nbd_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.694
r_scangle_it2.23
r_scbond_it1.366
r_angle_refined_deg1.118
r_mcangle_it0.877
r_angle_other_deg0.779
r_mcbond_it0.46
r_nbd_other0.228
r_symmetry_vdw_other0.201
r_nbd_refined0.199
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.136
r_symmetry_vdw_refined0.102
r_nbtor_other0.081
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3107
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing