1RWP

Crystal structure of human caspase-1 in complex with 3-{6-[(8-hydroxy-quinoline-2-carbonyl)-amino]-2-thiophen-2-yl-hexanoylamino}-4-oxo-butyric acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ICEPDB ID 1ICE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62780.1M PIPES, 175mM (NH4)2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.6854.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.216α = 90
b = 63.216β = 90
c = 161.694γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IV2003-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.22099.10.12317387
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)
12.22.2899.90.372

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ID 1ICE2.220173871606585697.320.213510.211830.24485RANDOM28.807
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]
1.111.11-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.121
r_scangle_it2.632
r_mcangle_it2.602
r_scbond_it1.6
r_mcbond_it1.492
r_angle_refined_deg0.902
r_nbd_refined0.164
r_symmetry_vdw_refined0.125
r_symmetry_hbond_refined0.119
r_xyhbond_nbd_refined0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.121
r_scangle_it2.632
r_mcangle_it2.602
r_scbond_it1.6
r_mcbond_it1.492
r_angle_refined_deg0.902
r_nbd_refined0.164
r_symmetry_vdw_refined0.125
r_symmetry_hbond_refined0.119
r_xyhbond_nbd_refined0.091
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2067
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing