9Y0A | pdb_00009y0a

Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold
experimental model	PDB	4A80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1 M HEPES pH 7.5; 0.05 M magnesium chloride hexahydrate; 30% PEG MME 550

Crystal Properties
Matthews coefficient	Solvent content
2.98	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.928	α = 90
b = 117.535	β = 90
c = 158.622	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER X 9M		2024-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	2.12	40	99.8	0.087	0.091	0.026	0.998	25.5	12.6		43908

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	2.12	2.16	99.7		0.73	0.764	0.224	0.866	2.1	11.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.12	39.694	43683	2224	99.783	0.173	0.1708	0.1842	0.2183	0.2254	RANDOM	59.23

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]
1.789			-0.775		-1.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.693
r_dihedral_angle_3_deg	11.323
r_lrange_other	9.948
r_lrange_it	9.939
r_dihedral_angle_2_deg	9.879
r_scangle_it	7.222
r_scangle_other	7.221
r_dihedral_angle_1_deg	6.98
r_scbond_it	5.226
r_scbond_other	5.225
r_mcangle_it	4.767
r_mcangle_other	4.767
r_mcbond_it	3.677
r_mcbond_other	3.676
r_angle_refined_deg	1.573
r_angle_other_deg	0.822
r_symmetry_nbd_other	0.212
r_nbd_other	0.203
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.195
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.174
r_chiral_restr	0.128
r_symmetry_nbd_refined	0.126
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.083
r_bond_other_d	0.011
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4457
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	76

Software

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