8VK2

X-ray crystal structure of human IgE 4C8 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MLH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	293	0.1 M Tris, 0.1 M sodium formate, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.009	α = 90
b = 80.664	β = 90
c = 164.807	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		2022-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	2.5	39.207	99.9	0.158	0.158	0.171	0.064	0.98	16.6	6.9		29122

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	99.9		0.708	0.708	0.773	0.307	0.819	2	5.8

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 7MLH	2.508	39.207	29068	1465	99.818	0.2	0.1978	0.2471	63.554

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]
-0.1			-3.385		3.485

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.465
r_dihedral_angle_3_deg	11.31
r_dihedral_angle_2_deg	8.549
r_lrange_it	7.924
r_lrange_other	7.917
r_dihedral_angle_1_deg	6.665
r_scangle_it	4.714
r_scangle_other	4.714
r_mcangle_other	4.032
r_mcangle_it	4.031
r_scbond_it	2.995
r_scbond_other	2.994
r_mcbond_it	2.547
r_mcbond_other	2.541
r_angle_refined_deg	1.22
r_angle_other_deg	0.417
r_nbd_other	0.307
r_symmetry_nbd_other	0.214
r_xyhbond_nbd_refined	0.214
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.172
r_ncsr_local_group_2	0.106
r_ncsr_local_group_1	0.103
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.052
r_symmetry_xyhbond_nbd_other	0.048
r_symmetry_xyhbond_nbd_refined	0.036
r_bond_refined_d	0.006
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	6247
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

Software

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