3D6H | pdb_00003d6h

Crystal structure of human caspase-1 with a naturally-occurring Asn263->Ser substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen. , VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.377	α = 90
b = 63.377	β = 90
c = 142.547	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	160	CCD	ADSC QUANTUM 315	Vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror	2006-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.98	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	20	96.8	0.074	7.9	3.8		19651

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	87.4		0.276	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1sc3	2	20	18630	1011	96.37	0.20174	0.19987	0.2	0.23659	0.24	RANDOM	27.63

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]
-1.54			-1.54		3.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.304
r_dihedral_angle_4_deg	15.764
r_dihedral_angle_3_deg	14.968
r_dihedral_angle_1_deg	5.891
r_scangle_it	4.353
r_mcangle_it	3.909
r_scbond_it	2.898
r_mcbond_it	2.679
r_angle_refined_deg	1.183
r_nbtor_refined	0.299
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2056
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement