9JE3 | pdb_00009je3

Structure of #2-911 Fab in complex with MEDI8852 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JW3
experimental model	PDB	2QHR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Bis-Tris (pH5.5), 13% PEG3350, 1% Tacsimate, 10 mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.283	α = 90
b = 151.111	β = 90
c = 176.368	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	273	PIXEL	DECTRIS PILATUS 6M		2024-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

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	2.374	48.43	88.8	0.038	0.999	12.72	2		91583

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.374	2.459			0.469	0.748

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	5JW3,2QHR	2.374	48.43	91583	4705	99.885	0.203	0.2	0.204	0.2543	0.2568	52.519

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]
-3.726			3.532		0.195

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.467
r_dihedral_angle_6_deg	13.801
r_lrange_it	12.741
r_lrange_other	12.741
r_dihedral_angle_2_deg	10.987
r_scangle_it	8.98
r_scangle_other	8.98
r_mcangle_other	7.815
r_mcangle_it	7.814
r_dihedral_angle_1_deg	7.235
r_scbond_it	5.985
r_scbond_other	5.975
r_mcbond_it	5.333
r_mcbond_other	5.325
r_angle_refined_deg	1.566
r_angle_other_deg	0.524
r_symmetry_xyhbond_nbd_refined	0.258
r_symmetry_nbd_other	0.207
r_nbd_refined	0.193
r_nbtor_refined	0.183
r_nbd_other	0.15
r_symmetry_nbd_refined	0.14
r_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.076
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13180
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	95

Software

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