7D8B

Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.01M Tri-sodium citrate, 16% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.595	α = 90
b = 140.394	β = 104.037
c = 61.961	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	PIXEL	DECTRIS EIGER X 9M		2019-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953700	Australian Synchrotron	MX1

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	2.46	70.197	99.9	0.177	3.6	7.7		28611

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	2.46	2.59			0.876	0.9

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2V8W	2.46	46.216	28587	1450	99.871	0.252	0.25	0.2918	34.813

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]
0.068		0.896	-2.743		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.797
r_dihedral_angle_3_deg	13.835
r_dihedral_angle_4_deg	13.569
r_dihedral_angle_1_deg	6.66
r_lrange_it	3.227
r_lrange_other	3.186
r_mcangle_it	2.107
r_mcangle_other	2.107
r_scangle_it	1.665
r_scangle_other	1.665
r_angle_refined_deg	1.185
r_mcbond_it	1.175
r_mcbond_other	1.175
r_angle_other_deg	1.076
r_scbond_it	0.933
r_scbond_other	0.933
r_symmetry_xyhbond_nbd_refined	0.225
r_symmetry_nbd_other	0.168
r_nbd_refined	0.162
r_nbtor_refined	0.152
r_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.134
r_nbd_other	0.133
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.037
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4817
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing