2C9U

1.24 Angstroms resolution structure of as-isolated Cu-Zn Human Superoxide dismutase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HL5PDB ENTRY 1HL5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
183.0 M AMMONIUM SULPHATE, 100 MM SODIUM CHLORITE, 50MM SODIUM ACETATE BUFFER, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.638α = 90
b = 67.553β = 106.48
c = 52.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2003-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.243096.30.06203.570045
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)
11.241.2892.50.42.22.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HL51.2450.1966500350195.80.1410.1390.176RANDOM12.39
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]
0.430.24-0.360.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.028
r_dihedral_angle_4_deg13.63
r_dihedral_angle_3_deg11.843
r_dihedral_angle_1_deg6.798
r_scangle_it4.618
r_scbond_it3.718
r_mcangle_it3.041
r_angle_other_deg2.495
r_mcbond_it2.417
r_angle_refined_deg1.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.028
r_dihedral_angle_4_deg13.63
r_dihedral_angle_3_deg11.843
r_dihedral_angle_1_deg6.798
r_scangle_it4.618
r_scbond_it3.718
r_mcangle_it3.041
r_angle_other_deg2.495
r_mcbond_it2.417
r_angle_refined_deg1.841
r_xyhbond_nbd_refined0.302
r_symmetry_hbond_refined0.297
r_nbd_refined0.253
r_nbd_other0.203
r_symmetry_vdw_refined0.193
r_symmetry_vdw_other0.182
r_nbtor_refined0.169
r_chiral_restr0.119
r_nbtor_other0.095
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms29

Software

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