8VQF | pdb_00008vqf

X-ray crystal structure of natural Can f 1 in complex with human IgE 1J11 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	8	293	2 M ammonium sulfate, 0.1 M Tris, pH 8

Crystal Properties
Matthews coefficient	Solvent content
4.73	73.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.758	α = 90
b = 154.758	β = 90
c = 89.415	γ = 120

Symmetry
Space Group	P 31 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		2021-10-12	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)	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	3.1	40	99.9	0.16	0.16	0.168	0.052	20.6	10		22392

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	3.1	3.15	100		1.079	1.079	1.132	0.339	0.89	2.1	11

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 7MLH	3.109	39.964	22377	1166	99.347	0.249	0.2479	0.2457	0.2681	0.2628	181.996

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]
1.54	0.77		1.54		-4.996

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.763
r_lrange_other	18.761
r_dihedral_angle_6_deg	11.908
r_scangle_other	11.526
r_scangle_it	11.425
r_dihedral_angle_3_deg	10.581
r_mcangle_it	7.937
r_mcangle_other	7.936
r_scbond_other	7.194
r_scbond_it	7.133
r_dihedral_angle_1_deg	6.086
r_mcbond_it	4.665
r_mcbond_other	4.665
r_dihedral_angle_2_deg	2.43
r_angle_other_deg	1.049
r_angle_refined_deg	0.938
r_nbd_other	0.231
r_symmetry_nbd_other	0.219
r_nbd_refined	0.195
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.104
r_symmetry_nbtor_other	0.095
r_symmetry_xyhbond_nbd_refined	0.052
r_chiral_restr	0.039
r_symmetry_xyhbond_nbd_other	0.028
r_gen_planes_other	0.012
r_gen_planes_refined	0.01
r_bond_refined_d	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4324
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	88

Software

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