3G76

Crystal structure of XIAP-BIR3 in complex with a bivalent compound

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	293	20% PEG MME 2000, 60mM sodium acetate tri-hydrate, 120mM Ammonium sulfate, 400mM sodium-potassium tartrate tetra-hydrate, pH 4.6, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.077	α = 90
b = 119.077	β = 90
c = 105.59	γ = 120

Symmetry
Space Group	P 31

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 315	Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror	2007-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3	40		0.101		3.6		33440

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3				0.64	2.2	3.7	4861

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	BIR3 DOMAIN FROM PDB ENTRY 3CLX	3	40	33415	1688	99.79	0.235	0.231	0.311	RANDOM	72.888

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]
2.66	1.33		2.66		-4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.397
r_dihedral_angle_3_deg	21.837
r_scangle_it	16.96
r_dihedral_angle_4_deg	12.595
r_scbond_it	12.204
r_mcangle_it	7.383
r_dihedral_angle_1_deg	4.985
r_mcbond_it	4.609
r_angle_refined_deg	2.042
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.397
r_dihedral_angle_3_deg	21.837
r_scangle_it	16.96
r_dihedral_angle_4_deg	12.595
r_scbond_it	12.204
r_mcangle_it	7.383
r_dihedral_angle_1_deg	4.985
r_mcbond_it	4.609
r_angle_refined_deg	2.042
r_chiral_restr	0.122
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6533
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	552

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.