2H48

Crystal structure of human caspase-1 (Cys362->Ala, Cys364->Ala, Cys397->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SC3PDB ENTRY 1SC3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62770.1M Pipes pH 6.0, 200 mM ammonium sulfate, 25% PEG 2000 MME, 10 mM DTT, 2 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6653.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.006α = 90
b = 63.006β = 90
c = 161.279γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV2003-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.22097.5168022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2899.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SC32.220163721559382995.240.216740.216740.213920.27242RANDOM35.929
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]
1.051.05-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.927
r_dihedral_angle_4_deg15.628
r_dihedral_angle_3_deg15.555
r_dihedral_angle_1_deg4.99
r_mcangle_it2.744
r_scangle_it2.462
r_mcbond_it1.608
r_scbond_it1.498
r_angle_refined_deg0.952
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.927
r_dihedral_angle_4_deg15.628
r_dihedral_angle_3_deg15.555
r_dihedral_angle_1_deg4.99
r_mcangle_it2.744
r_scangle_it2.462
r_mcbond_it1.608
r_scbond_it1.498
r_angle_refined_deg0.952
r_nbtor_refined0.295
r_nbd_refined0.168
r_symmetry_vdw_refined0.133
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.113
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2097
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing