2H9G

Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D0G	Chain S from 1d0g Chain AB from 1FVE
experimental model	PDB	1FVE	Chain S from 1d0g Chain AB from 1FVE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.814	α = 90
b = 61.389	β = 101.17
c = 108.269	γ = 90

Symmetry
Space Group	P 1 21 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		2003-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.00	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	50	97.1	0.089	6.7	3.4	54784	54784	-3	-3

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)
1	2.3	2.38	97.3		0.419	2	3.8	5470

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Chain S from 1d0g Chain AB from 1FVE	2.32	30	-3	54443	48957	5486	97	0.2338	0.2338	0.22846	0.28164	RANDOM	12.83

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]
0.47		0.66	-1.09		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.303
r_dihedral_angle_4_deg	18.841
r_dihedral_angle_3_deg	17.824
r_dihedral_angle_1_deg	6.57
r_scangle_it	3.45
r_mcangle_it	3.326
r_mcbond_it	2.47
r_scbond_it	2.413
r_angle_refined_deg	1.3
r_angle_other_deg	0.766
r_mcbond_other	0.515
r_nbd_refined	0.192
r_symmetry_vdw_other	0.19
r_nbd_other	0.181
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.118
r_nbtor_other	0.083
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7756
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms

Software

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