8VK1

X-ray crystal structure of human IgE 4C8 Fab complex with Der p 2.0103

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	4	293	1.0 M lithium chloride, 0.3 M citrate, pH 4.0, 25% w/v PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.93	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.254	α = 90
b = 95.298	β = 105.724
c = 69.209	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 EIGER2 XE 16M		2022-02-22	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	3.05	40	99	0.105	0.105	0.122	0.061	0.984	13.7	3.8		26735

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	3.05	3.1	97.1		0.42	0.42	0.49	0.25	0.82	1.8

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	3.05	39.577	26651	1353	98.532	0.199	0.1967	0.2477	68.809

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]
-1.691		-1.523	6.208		-3.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.338
r_dihedral_angle_3_deg	11.907
r_dihedral_angle_2_deg	8.174
r_lrange_it	7.535
r_lrange_other	7.535
r_dihedral_angle_1_deg	6.291
r_mcangle_it	3.576
r_mcangle_other	3.576
r_scangle_it	3.465
r_scangle_other	3.465
r_mcbond_it	2.078
r_mcbond_other	2.078
r_scbond_it	2.02
r_scbond_other	2.02
r_angle_refined_deg	1.302
r_angle_other_deg	0.448
r_symmetry_xyhbond_nbd_refined	0.431
r_nbd_other	0.27
r_symmetry_nbd_refined	0.256
r_xyhbond_nbd_refined	0.226
r_symmetry_nbd_other	0.218
r_nbd_refined	0.205
r_nbtor_refined	0.174
r_ncsr_local_group_1	0.144
r_ncsr_local_group_2	0.128
r_ncsr_local_group_3	0.118
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.057
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8356
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

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