2CW3

X-ray structure of PmSOD2, superoxide dismutase from Perkinsus marinus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52980.17M Sodium Acetate trihydrate, 0.085M Tris Hydrochloride at pH 8.5, 25.5% w/v PEG 4000 and 15% glycerol, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.43α = 90
b = 73.894β = 90
c = 94.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.529.596.70.0862081717422
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)
2.52.5792.90.332.63

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.529.211418073396.690.185490.181850.25712RANDOM15.739
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]
-0.130.020.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.519
r_dihedral_angle_4_deg19.185
r_dihedral_angle_3_deg18.71
r_dihedral_angle_1_deg5.623
r_scangle_it2.509
r_scbond_it1.61
r_angle_refined_deg1.408
r_mcangle_it1.178
r_mcbond_it0.693
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.519
r_dihedral_angle_4_deg19.185
r_dihedral_angle_3_deg18.71
r_dihedral_angle_1_deg5.623
r_scangle_it2.509
r_scbond_it1.61
r_angle_refined_deg1.408
r_mcangle_it1.178
r_mcbond_it0.693
r_nbtor_refined0.315
r_symmetry_hbond_refined0.263
r_symmetry_vdw_refined0.247
r_nbd_refined0.234
r_xyhbond_nbd_refined0.188
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms3209
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing