9NPH | pdb_00009nph

X-ray crystal structure of recombinant Can f 1 in complex with human IgE mAb 1J11 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8VQF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M Lithium sulfate monohydrate, 0.1 M HEPES , 25% w/v PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.67	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.511	α = 90
b = 69.511	β = 90
c = 247.04	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 EIGER X 9M		2024-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.979	NSLS-II	17-ID-1

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	2.59	40	91.6	0.122	0.128	0.037	0.979	15.9	9.9		20567

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	2.59	2.63	93.2		0.66	0.691	0.192	0.995		9.6

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	2.592	38.221	20507	1013	91.459	0.218	0.2153	0.219	0.261	0.2632	56.963

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]
0.172	0.086		0.172		-0.559

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.556
r_dihedral_angle_6_deg	12.236
r_lrange_it	10.22
r_lrange_other	10.182
r_dihedral_angle_2_deg	8.866
r_dihedral_angle_1_deg	7.577
r_scangle_it	6.907
r_scangle_other	6.473
r_mcangle_it	5.708
r_mcangle_other	5.707
r_scbond_it	4.542
r_scbond_other	4.212
r_mcbond_it	3.532
r_mcbond_other	3.532
r_angle_refined_deg	1.506
r_angle_other_deg	0.953
r_nbd_other	0.378
r_xyhbond_nbd_refined	0.303
r_symmetry_nbd_other	0.235
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.221
r_nbtor_refined	0.178
r_symmetry_nbtor_other	0.094
r_symmetry_xyhbond_nbd_refined	0.088
r_chiral_restr	0.071
r_gen_planes_other	0.013
r_symmetry_xyhbond_nbd_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4373
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	109

Software

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