1PAU | pdb_00001pau

Crystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ICE	PROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5		HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.47	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.81	α = 90
b = 84.62	β = 90
c = 96.79	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	AREA DETECTOR	SIEMENS		1995-11-09	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	36	87.1	0.0634	0.0555	17.4	2.33		8929			31.34

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	87.1		0.257	0.262	2.59	2.27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE-R	PROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE)	2.5	20	2	7987	845	78	0.195	0.195	0.18	0.275	RANDOM	23.56

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	24.14
x_angle_deg	1.308
x_improper_angle_d	1.091
x_bond_d	0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1905
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SAINT	data reduction
SAINT	data scaling
X-PLOR	phasing