8DGR

Crystal Structure of scFv(F8) Antibody Fragment

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	1.8 M ammonium sulfate, 0.2 M magnesium chloride, 0.1 M HEPES, 5 % glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.644	α = 90
b = 119.644	β = 90
c = 74.856	γ = 90

Symmetry
Space Group	I 41 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	100	PIXEL	DECTRIS PILATUS 6M		2022-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979340	APS	19-ID

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	1.56	43.53	99.6	0.1748	10708.8	19.1		367580

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	1.56	1.6	95.52		0.172

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5B3N	1.56	43.53	38641	1883	99.611	0.176	0.1748	0.1949	RANDOM	15.299

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]
-0.002			-0.002		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.116
r_dihedral_angle_3_deg	12.641
r_dihedral_angle_2_deg	10.886
r_dihedral_angle_1_deg	6.539
r_lrange_it	5.508
r_lrange_other	5.496
r_scangle_it	4.788
r_scangle_other	4.786
r_scbond_it	3.283
r_scbond_other	3.282
r_mcangle_it	2.22
r_mcangle_other	2.219
r_angle_refined_deg	1.736
r_mcbond_it	1.605
r_mcbond_other	1.521
r_angle_other_deg	0.616
r_symmetry_nbd_refined	0.237
r_symmetry_nbd_other	0.198
r_nbd_refined	0.197
r_nbtor_refined	0.182
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1845
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing