5D93 | pdb_00005d93

Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Fragment from a Mouse QSOX1-Specific Antibody

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D8I	5D8I, 3D85, 4Q0X, 3AB0
experimental model	PDB	3D85	5D8I, 3D85, 4Q0X, 3AB0
experimental model	PDB	4Q0X	5D8I, 3D85, 4Q0X, 3AB0
experimental model	PDB	3AB0	5D8I, 3D85, 4Q0X, 3AB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	50 mM ammonium sulfate, 0.1 M bis-tris methane buffer, pH 5.5, 22% w/v PEG 3.35 kD

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.539	α = 90
b = 112.715	β = 90
c = 193.418	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2015-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	50	98.9	0.088	0.088	7.6	4.9		72630		-3

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)
1	2.2	2.24	98.8		0.408	2	3.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5D8I, 3D85, 4Q0X, 3AB0	2.201	23.203	1.34	72573	3588	98.88	0.1771	0.174	0.18	0.2362	0.18	random selection	32.65

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	13.349
f_angle_d	1.113
f_chiral_restr	0.041
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10156
Nucleic Acid Atoms
Solvent Atoms	751
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.