8XX0 | pdb_00008xx0

Crystal structure of anti-IgE antibody HMK-12 Fab complexed with IgE F(ab')2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I9I	1i9i, 2vxq, 1o0v,
experimental model	PDB	2VXQ	1i9i, 2vxq, 1o0v,
experimental model	PDB	1O0V	1i9i, 2vxq, 1o0v,

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	14 %(w/v) PEG3350, 0.09 M MES-NaOH(pH6.5), 0.09 M Magnesium acetate, 0.09 %(w/v) beta-octylglucoside, 0.1 M NDSB-256

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 282.05	α = 90
b = 86.09	β = 97.19
c = 56.06	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 EIGER X 9M		2021-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	0.99999	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.9	49.6	99.85	0.466	0.996	17.77	63.9		29738			43.82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	99.7		2.584	0.898	2.93	65.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1i9i, 2vxq, 1o0v,	2.9	49.6	1.35	29703	1920	99.87	0.2279	0.2253	0.2336	0.2671	0.2701	64.91

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.6467
f_angle_d	0.6224
f_chiral_restr	0.0432
f_plane_restr	0.0052
f_bond_d	0.0022

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7355
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	84

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing