Experiment: 8TCA

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, no ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MFB	HIGH RESOLUTION STRUCTURES OF ANTIBODY FAB FRAGMENT COMPLEXED WITH CELL-SURFACE OLIGOSACCHARIDE OF PATHOGENIC SALMONELLA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	PEG 2K [20% (v/v)], MgCl2 [0.2 M], Tris pH 8.0 [0.1 M], glycerol [5-15% (v/v)]

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.906	α = 90
b = 79.906	β = 90
c = 145.127	γ = 90

Symmetry
Space Group	P 43 21 2

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		2023-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	2.02	70	98.24	0.2183	0.2341	0.08188	0.996	9.71	7.4		31198			27.12

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	2.02	2.092	96.71		2.29	2.466	0.8885	0.546	1.08	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.02	70	1.34	31042	1547	98.23	0.1835	0.1814	0.185	0.2243	0.2267	RANDOM	33.8

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	13.9104
f_angle_d	1.1827
f_chiral_restr	0.071
f_plane_restr	0.0185
f_bond_d	0.0094

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3236
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	36

Software

Software
Software Name	Purpose
PDB-REDO	refinement
PHENIX	refinement
autoPROC	data processing
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building