9Y0D | pdb_00009y0d

Crystal structure of human IgE Fab 2H22

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9Y0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	277	0.1 M citric acid pH 3.5; 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.769	α = 90
b = 116.769	β = 90
c = 71.102	γ = 120

Symmetry
Space Group	P 65

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 X 16M		2025-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.729	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.27	40	99.3	0.144	0.153	0.048	0.987	47.9	11.1		25393

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27	2.31	100		0.911	0.951	0.268	0.834	2.2	12.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.27	27.019	25366	1189	98.831	0.189	0.187	0.1972	0.2435	0.2525	79.42

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]
0.462	0.231		0.462		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	11.737
r_dihedral_angle_3_deg	10.972
r_dihedral_angle_2_deg	7.285
r_dihedral_angle_1_deg	7.252
r_lrange_it	6.6
r_lrange_other	6.587
r_scangle_it	3.689
r_scangle_other	3.688
r_mcangle_it	3.332
r_mcangle_other	3.331
r_scbond_it	2.398
r_scbond_other	2.397
r_mcbond_it	2.127
r_mcbond_other	2.127
r_angle_refined_deg	0.991
r_angle_other_deg	0.44
r_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.207
r_nbd_other	0.2
r_nbd_refined	0.191
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.118
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.055
r_bond_other_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3220
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing