6ZEC

Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	25 %w/v Polyethylene Glycol 3350 0.200 M Magnesium Chloride 0.100 M bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.33	α = 90
b = 60.79	β = 90
c = 84.17	γ = 90

Symmetry
Space Group	P 21 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 EIGER2 XE 16M		2018-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	50.61	100	0.082	0.99	13.8	6.4		57128

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69	100		0.49	1	6.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5NIV	1.65	50.61	54318	2765	99.97	0.17622	0.1747	0.20605	RANDOM	25.273

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]
0.59			0.33		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.434
r_dihedral_angle_4_deg	16.568
r_dihedral_angle_1_deg	16.225
r_dihedral_angle_3_deg	11.939
r_long_range_B_refined	4.91
r_long_range_B_other	4.625
r_scangle_other	2.358
r_mcangle_it	1.815
r_mcangle_other	1.815
r_scbond_it	1.462
r_scbond_other	1.462
r_angle_refined_deg	1.461
r_angle_other_deg	1.346
r_mcbond_it	1.099
r_mcbond_other	1.096
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	3386
Nucleic Acid Atoms
Solvent Atoms	433
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing