3KJF | pdb_00003kjf

Caspase 3 Bound to a covalent inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	277	Inhibitor (2 microliters of a 100 mM DMSO stock) added to 100 microliters of protein (6.5 mg/mL) in 20 mM Tris, 10 mM DTT pH 8.0. Drops contained equal volumes of protein and well solution (16% ethanol, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.69	α = 90
b = 68.16	β = 90
c = 44.77	γ = 90

Symmetry
Space Group	P 21 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	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	2	20	89.2			20643	16700			15.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.05	60.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	18.71	20643	16700	1822	89.2	0.18322	0.18322	0.18068	0.2101	0.20649	0.2315	RANDOM	15.373

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]
-2.75			-0.85		3.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.981
r_dihedral_angle_4_deg	16.573
r_dihedral_angle_3_deg	13.216
r_dihedral_angle_1_deg	6.037
r_scangle_it	2.117
r_scbond_it	1.351
r_angle_refined_deg	1.347
r_angle_other_deg	0.841
r_mcangle_it	0.799
r_mcbond_it	0.426
r_mcbond_other	0.094
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1940
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	43

Software

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