3KJQ | pdb_00003kjq

Caspase 8 with covalent inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	277	2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.974	α = 90
b = 63.974	β = 90
c = 130.847	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	1.8	20	99.6			29350	29346

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.85	96.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	19.94	26415	2933	99.59	0.1846	0.18208	0.1876	0.20719	0.2116	RANDOM	12.497

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]
0.64	0.32		0.64		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.464
r_dihedral_angle_4_deg	15.512
r_dihedral_angle_3_deg	12.755
r_dihedral_angle_1_deg	5.966
r_scangle_it	2.968
r_scbond_it	1.924
r_angle_refined_deg	1.242
r_mcangle_it	1.205
r_angle_other_deg	0.877
r_mcbond_it	0.751
r_symmetry_vdw_other	0.224
r_nbd_refined	0.19
r_nbd_other	0.181
r_nbtor_refined	0.18
r_symmetry_vdw_refined	0.162
r_mcbond_other	0.137
r_symmetry_hbond_refined	0.126
r_xyhbond_nbd_refined	0.116
r_nbtor_other	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1924
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling