8S6V | pdb_00008s6v

Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	lithium sulfate Bis-Tris PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.053	α = 90
b = 111.546	β = 90
c = 134.962	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	PIXEL	DECTRIS PILATUS3 S 6M		2022-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	134.96	100	0.075	0.993	7.1	5.2		74559

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.06	100		0.573	0.599	1.5	5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.95	85.98	71315	3113	99.89	0.20124	0.1994	0.2071	0.2441	0.2492	RANDOM	29.964

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]
0.63			-2.64		2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.636
r_dihedral_angle_2_deg	8.056
r_dihedral_angle_1_deg	7.174
r_long_range_B_refined	6.781
r_long_range_B_other	6.668
r_scangle_other	5.073
r_scbond_it	3.439
r_scbond_other	3.371
r_mcangle_other	3.362
r_mcangle_it	3.361
r_mcbond_it	2.333
r_mcbond_other	2.332
r_angle_refined_deg	1.445
r_angle_other_deg	0.782
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6582
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms	233

Software

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