2C9S

1.24 Angstroms resolution structure of Zn-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
14.752.5M AMMONIUM SULPHATE,0.1M NACL,50MM ACETATE BUFFER, pH 4.75
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.243α = 90
b = 67.742β = 106.44
c = 51.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2003-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.2430960.06183.267983
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)
11.241.2878.40.372.32.2

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 1HL51.2419.965893206195.90.1540.1520.194RANDOM10.82
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]
-0.860.030.070.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.256
r_dihedral_angle_3_deg14.8
r_dihedral_angle_1_deg13.34
r_dihedral_angle_4_deg9.233
r_scangle_it4.468
r_scbond_it3.501
r_mcangle_it2.619
r_angle_other_deg2.248
r_mcbond_it2.18
r_angle_refined_deg2.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.256
r_dihedral_angle_3_deg14.8
r_dihedral_angle_1_deg13.34
r_dihedral_angle_4_deg9.233
r_scangle_it4.468
r_scbond_it3.501
r_mcangle_it2.619
r_angle_other_deg2.248
r_mcbond_it2.18
r_angle_refined_deg2.105
r_symmetry_vdw_refined0.308
r_symmetry_hbond_refined0.272
r_xyhbond_nbd_refined0.266
r_nbd_refined0.26
r_symmetry_vdw_other0.221
r_nbd_other0.21
r_nbtor_refined0.171
r_chiral_restr0.127
r_nbtor_other0.099
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms2222
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms48

Software

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