7UEN | pdb_00007uen

Genetic and structural basis of the human anti-alpha-galactosyl antibody response

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N8Z	Fab arm first split into variable and constant pairings

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Equal volumes of a protein (in 25 mM Tris (pH 8.0), 100 mM NaCl) and well solution (1.5 M NaH2PO4.H2O.K2HPO4, pH 8.0) were combined.

Crystal Properties
Matthews coefficient	Solvent content
2.36	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.492	α = 90
b = 101.492	β = 90
c = 78.159	γ = 120

Symmetry
Space Group	P 32 2 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 16M		2017-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	38.31	100	0.091	0.093	0.021	0.999	17.2	18.9		67630

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	99.9		1.757	1.822	0.475	0.465		14.3

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 (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	THROUGHOUT	generic Fab	1.55	38.31	64307	3288	99.96	0.1298	0.1276	0.14	0.1747	0.19	RANDOM	27.962

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]
0.17	0.08		0.17		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.129
r_dihedral_angle_4_deg	20.351
r_dihedral_angle_3_deg	12.178
r_dihedral_angle_1_deg	7.237
r_rigid_bond_restr	3.296
r_angle_refined_deg	1.681
r_angle_other_deg	1.452
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.129
r_dihedral_angle_4_deg	20.351
r_dihedral_angle_3_deg	12.178
r_dihedral_angle_1_deg	7.237
r_rigid_bond_restr	3.296
r_angle_refined_deg	1.681
r_angle_other_deg	1.452
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3196
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	45

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.