8FWH | pdb_00008fwh

Crystal structure of bivalent antibody Fab fragment of Anti-human LAG3 (22D2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WKM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.1 M Tris-HCl, pH 7.5, 0.2 M sodium chloride, 10% w/v PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.287	α = 90
b = 44.39	β = 106.136
c = 89.084	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 PILATUS 6M		2021-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.83	85.57	92.9	0.98	13.7	2		13587

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	2.83	2.9			0.68

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 6WKM	2.833	42.75	13587	706	92.903	0.219	0.2164	0.22	0.2767	0.27	77.32

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]
-3.808		-1.694	10.894		-5.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.039
r_dihedral_angle_4_deg	18.474
r_dihedral_angle_3_deg	17.024
r_lrange_it	15.314
r_lrange_other	15.303
r_scangle_it	9.767
r_scangle_other	9.765
r_mcangle_it	9.182
r_mcangle_other	9.18
r_dihedral_angle_1_deg	7.019
r_scbond_it	6.332
r_scbond_other	6.33
r_mcbond_it	6.035
r_mcbond_other	6.034
r_angle_refined_deg	1.397
r_angle_other_deg	1.279
r_symmetry_xyhbond_nbd_refined	0.275
r_xyhbond_nbd_other	0.27
r_nbd_refined	0.236
r_symmetry_nbd_other	0.204
r_nbd_other	0.191
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.152
r_xyhbond_nbd_refined	0.146
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3145
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing