8AON | pdb_00008aon

Oxidoreductase fragment of human QSOX1 in complex with a Fab fragment of a humanized anti-QSOX1 antibody

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG 4000, ammonium phosphate dibasic

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.168	α = 90
b = 98.721	β = 101.19
c = 63.09	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	77	PIXEL	DECTRIS PILATUS3 6M		2022-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9763	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.1	49.36	97	0.105	0.075	6.8	2.7		102949			46.08

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	98.55		1.127		2.82

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4IJ3	2.1	49.36	1.25	77284	7728	99.62	0.2039	0.1978	0.2	0.259	0.26	55.26

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.2952
f_angle_d	0.9083
f_chiral_restr	0.0552
f_plane_restr	0.0081
f_bond_d	0.0073

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5005
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building