2H4W

Crystal structure of human caspase-1 (Glu390->Asp) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.1 M PIPES, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.67	54.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.214	α = 90
b = 63.214	β = 90
c = 161.328	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	110	IMAGE PLATE	RIGAKU RAXIS IV		2005-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	92				21109	1	5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	98.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SC3	2	20	21065	19985	1079	91.8	0.238	0.21212	0.21029	0.2466	RANDOM	26.197

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]
0.86			0.86		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.035
r_scangle_it	2.411
r_mcangle_it	2.394
r_scbond_it	1.472
r_mcbond_it	1.38
r_angle_refined_deg	0.888
r_nbd_refined	0.158
r_symmetry_vdw_refined	0.12
r_symmetry_hbond_refined	0.081
r_xyhbond_nbd_refined	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.035
r_scangle_it	2.411
r_mcangle_it	2.394
r_scbond_it	1.472
r_mcbond_it	1.38
r_angle_refined_deg	0.888
r_nbd_refined	0.158
r_symmetry_vdw_refined	0.12
r_symmetry_hbond_refined	0.081
r_xyhbond_nbd_refined	0.08
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2052
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.