1RWM

Crystal structure of human caspase-1 in complex with 4-oxo-3-[2-(5-{[4-(quinoxalin-2-ylamino)-benzoylamino]-methyl}-thiophen-2-yl)-acetylamino]-pentanoic 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, 200mM Li2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.221α = 90
b = 63.221β = 90
c = 161.164γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IV2003-01-24MSINGLE 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
12.72097.20.1289552
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)
12.72.7998.60.382

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 1ICE2.7209552876643796.340.201910.199340.25437RANDOM33.988
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]
1.491.49-2.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.038
r_mcangle_it3.284
r_scangle_it3.024
r_mcbond_it1.89
r_scbond_it1.781
r_angle_refined_deg1.111
r_nbd_refined0.174
r_symmetry_vdw_refined0.133
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.038
r_mcangle_it3.284
r_scangle_it3.024
r_mcbond_it1.89
r_scbond_it1.781
r_angle_refined_deg1.111
r_nbd_refined0.174
r_symmetry_vdw_refined0.133
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.122
r_chiral_restr0.06
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 Atoms2069
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing