2JLP | pdb_00002jlp

Crystal structure of human extracellular copper-zinc superoxide dismutase.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C9VPDB ENTRY 2C9V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PEG3350, THIOCYANATE, BIS-TRIS PROPANE PH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9336.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.738α = 90
b = 93.588β = 106.23
c = 75.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-09-22MSINGLE 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
11.728.297.30.06163.78105620.8
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)
11.71.76800.332.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C9V1.728.276936405797.20.1520.150.160.1850.19RANDOM24.02
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]
-1.24-0.561.29-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.6
r_dihedral_angle_4_deg16.287
r_dihedral_angle_3_deg11.711
r_dihedral_angle_1_deg6.837
r_scangle_it3.834
r_scbond_it2.475
r_angle_refined_deg1.71
r_mcangle_it1.667
r_mcbond_it1.01
r_angle_other_deg0.996
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4954
Nucleic Acid Atoms
Solvent Atoms889
Heterogen Atoms14

Software

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