1SC4

Crystal structure of the human caspase-1 C285A mutant after removal of malonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RWNPDB ENTRY 1RWN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72742 M sodium malonate, VAPOR DIFFUSION, HANGING DROP, temperature 274K. Malonate-bound enzyme crystals were transferred into mother liquor composed of 0.1 M PIPES pH 6, 88 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3 and 2 mM MgCl2, and soaked for 2 days to remove malonate.
Crystal Properties
Matthews coefficientSolvent content
2.3647.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.982α = 90
b = 62.982β = 90
c = 143.158γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IV2003-07-10MSINGLE 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
12.12095.30.1117527
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)
12.12.1778.60.297

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 ENTRY 1RWN2.120175271587383395.310.222950.221060.2584RANDOM23.579
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.426
r_mcangle_it2.763
r_scangle_it2.711
r_scbond_it1.662
r_mcbond_it1.598
r_angle_refined_deg0.911
r_nbd_refined0.161
r_symmetry_vdw_refined0.137
r_symmetry_hbond_refined0.095
r_xyhbond_nbd_refined0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.426
r_mcangle_it2.763
r_scangle_it2.711
r_scbond_it1.662
r_mcbond_it1.598
r_angle_refined_deg0.911
r_nbd_refined0.161
r_symmetry_vdw_refined0.137
r_symmetry_hbond_refined0.095
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 Atoms1956
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing