X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ICEPROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop
Crystal Properties
Matthews coefficientSolvent content
2.4751

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.81α = 90
b = 84.62β = 90
c = 96.79γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293AREA DETECTORSIEMENS1995-11-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.53687.10.06340.055517.42.33892931.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5987.10.2570.2622.592.27

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-RPROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE)2.52027987845780.1950.1950.275RANDOM23.56
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
x_dihedral_angle_d24.14
x_angle_deg1.308
x_improper_angle_d1.091
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.14
x_angle_deg1.308
x_improper_angle_d1.091
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1905
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing