8OG0

Crystal structure of MJF14-6-4-2 Fab fragment in complex with epitope peptide

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	Sitting droplets were set up by mixing 1 ul of Fab fragments, 0.5 ul of peptide (1 mg/ml in 20 mM tris-HCl) and 1 ul crystallization buffer (24% PEG 6000, 0.1M Na-citrate pH 5.0).

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.484	α = 90
b = 66.7	β = 90
c = 167.167	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 EIGER2 XE 16M		2023-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.712	83.58	94.3	0.208	8.5	13		37216

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	1.712	1.902			1.609

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.712	83.58	30930	1594	70.39	0.19704	0.19531	0.23117	RANDOM	22.835

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			0.16		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.487
r_dihedral_angle_1_deg	7.655
r_dihedral_angle_2_deg	6.766
r_long_range_B_refined	4.702
r_long_range_B_other	4.651
r_scangle_other	3.266
r_mcangle_it	2.937
r_mcangle_other	2.936
r_scbond_it	2.189
r_scbond_other	2.188
r_mcbond_it	1.936
r_mcbond_other	1.935
r_angle_refined_deg	1.361
r_angle_other_deg	0.477
r_chiral_restr	0.063
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
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	3211
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing