2AWP

Crystal structure of Plasmodium knowlesi structure of Iron Super-Oxide Dismutase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AO3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.129730%PEG4K,0.2M NH4 Acetate,0.1M Na Cacodylate,5mM MnCl2, pH 5.1, VAPOR DIFFUSION, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.141.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.24α = 90
b = 79.053β = 90
c = 88.672γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVeriMax2005-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
125099.10.1570.1574.952677026770
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)
22.0390.70.5780.5782.434.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2AO32502563825638109199.450.16090.158170.2254RANDOM14.707
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]
0.02-0.940.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.98
r_dihedral_angle_3_deg13.434
r_dihedral_angle_1_deg5.998
r_dihedral_angle_4_deg5.586
r_scangle_it3.11
r_scbond_it2.077
r_angle_refined_deg1.355
r_mcangle_it1.252
r_mcbond_it0.785
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.98
r_dihedral_angle_3_deg13.434
r_dihedral_angle_1_deg5.998
r_dihedral_angle_4_deg5.586
r_scangle_it3.11
r_scbond_it2.077
r_angle_refined_deg1.355
r_mcangle_it1.252
r_mcbond_it0.785
r_nbtor_refined0.305
r_nbd_refined0.199
r_symmetry_hbond_refined0.193
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.145
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3177
Nucleic Acid Atoms
Solvent Atoms559
Heterogen Atoms5

Software

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