1SC3

Crystal structure of the human caspase-1 C285A mutant in complex with 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
Crystal Properties
Matthews coefficientSolvent content
2.6954.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.115α = 90
b = 63.115β = 90
c = 162.461γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IV2003-05-22MSINGLE 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
11.82097.570.05831330
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)
11.81.8694.50.288

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 1RWN1.8203133029025154497.570.207120.205470.23806RANDOM22.618
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]
0.560.56-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.012
r_scangle_it2.514
r_mcangle_it2.259
r_scbond_it1.505
r_mcbond_it1.241
r_angle_refined_deg0.845
r_nbd_refined0.159
r_symmetry_vdw_refined0.12
r_symmetry_hbond_refined0.109
r_xyhbond_nbd_refined0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.012
r_scangle_it2.514
r_mcangle_it2.259
r_scbond_it1.505
r_mcbond_it1.241
r_angle_refined_deg0.845
r_nbd_refined0.159
r_symmetry_vdw_refined0.12
r_symmetry_hbond_refined0.109
r_xyhbond_nbd_refined0.079
r_chiral_restr0.056
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 Atoms2068
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing