4XDX

The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IL8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62910.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 20% w/v Polyethylene glycol 4,000, 15% v/v Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5151.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.093α = 90
b = 40.093β = 90
c = 89.269γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702009-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.806NSLSX6A

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
10.95899.50.0537.818.7529298.52
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)
10.950.971000.7432.38.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3il80.957.9391.3452700263599.210.12160.12080.1356random15.1823
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.319
f_angle_d2.132
f_chiral_restr0.106
f_bond_d0.025
f_plane_restr0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms571
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms6

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling