1Z6T

Structure of the apoptotic protease-activating factor 1 bound to ADP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.1	276	HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10

Crystal Properties
Matthews coefficient	Solvent content
2.4	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.955	α = 62.96
b = 92.883	β = 89.99
c = 94.988	γ = 90.05

Symmetry
Space Group	P 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 4		2004-07-01	M	SINGLE WAVELENGTH
2	1	x-ray		M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1
2	SYNCHROTRON	CHESS BEAMLINE A1	1.0088, 0.9500, 1.0053	CHESS	A1

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	2.2	50	89.5	0.048	0.048	12.7	1.7		103300

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.21	2.27	48.9		0.267	2.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.21	15	102933	97722	5211	89.2	0.192	0.189	0.244	RANDOM	36.38

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]
0.18	0.13	0.77	0.4	-0.45	-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.382
r_dihedral_angle_4_deg	22.503
r_dihedral_angle_3_deg	16.481
r_scangle_it	6.432
r_dihedral_angle_1_deg	6.191
r_scbond_it	4.687
r_mcangle_it	2.682
r_mcbond_it	2.19
r_angle_refined_deg	1.431
r_angle_other_deg	0.872
r_symmetry_hbond_refined	0.306
r_symmetry_vdw_refined	0.277
r_symmetry_vdw_other	0.261
r_mcbond_other	0.239
r_xyhbond_nbd_other	0.23
r_xyhbond_nbd_refined	0.213
r_nbd_refined	0.209
r_nbd_other	0.181
r_nbtor_refined	0.175
r_nbtor_other	0.088
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18752
Nucleic Acid Atoms
Solvent Atoms	803
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing