8P6I

Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide epitope

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		By ColabFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	0.2M NaCl 20%w/v PEG 8K 0.1M Na Phos Cit pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.833	α = 90
b = 42.757	β = 122.306
c = 129.064	γ = 90

Symmetry
Space Group	C 1 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 EIGER2 X CdTe 9M		2023-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6199	Diamond	I24

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	2.5	56.117	100	0.387	0.399	0.093	0.988	9	18.2		34554

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	2.5	2.6	100		1.813	1.876	0.478	0.689	0.7	15.3

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	56.117	34554	1758	99.945	0.206	0.2031	0.2538	32.858

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]
0.556		0.246	-0.684		-0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.966
r_dihedral_angle_3_deg	16.104
r_dihedral_angle_2_deg	8.414
r_dihedral_angle_1_deg	8.008
r_lrange_it	4.202
r_lrange_other	4.181
r_scangle_it	2.884
r_scangle_other	2.884
r_mcangle_it	2.459
r_mcangle_other	2.459
r_scbond_it	1.709
r_scbond_other	1.708
r_mcbond_it	1.429
r_mcbond_other	1.429
r_angle_refined_deg	1.325
r_angle_other_deg	0.441
r_symmetry_xyhbond_nbd_refined	0.242
r_symmetry_nbd_other	0.201
r_nbd_refined	0.195
r_nbd_other	0.191
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.162
r_ncsr_local_group_1	0.097
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_2	0.08
r_symmetry_xyhbond_nbd_other	0.073
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6719
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2.multiplex	data reduction
Aimless	data scaling
PHASER	phasing