5JKC | pdb_00005jkc

Crystal structure of human IZUMO1-JUNO complex (crystal form 1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JK9	5JK9, 5JKA
experimental model	PDB	5JKA	5JK9, 5JKA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	8-12% PEG4000, 0.2 M Li2SO4, 0.1 M MES-NaOH pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.188	α = 90
b = 144.75	β = 90
c = 141.88	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 PILATUS 2M-F		2015-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.9	50	100	34.5	6.5		15228

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 (Observed)	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	5JK9, 5JKA	2.9	50	14419	787	99.81	0.2273	0.22547	0.23	0.25941	0.26	RANDOM	105.131

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]
0.73			2.42		-3.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.139
r_dihedral_angle_3_deg	17.106
r_dihedral_angle_4_deg	15.512
r_long_range_B_refined	11.361
r_long_range_B_other	11.36
r_dihedral_angle_1_deg	6.926
r_scangle_other	5.291
r_mcangle_it	5.247
r_mcangle_other	5.246
r_mcbond_it	3.159
r_mcbond_other	3.159
r_scbond_it	3.101
r_scbond_other	3.1
r_angle_refined_deg	1.648
r_angle_other_deg	1.037
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3488
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	29

Software

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