5JKD | pdb_00005jkd

Crystal structure of human IZUMO1-JUNO complex (crystal form 2)

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	1.0 M (NH4)2SO4, 1.0 M KCl, 0.1 M HEPES-NaOH pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.604	α = 90
b = 65.377	β = 104.24
c = 77.199	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 PILATUS 2M-F		2016-03-12	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	99.9	21.6	6.6		15805

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	15006	799	99.77	0.22169	0.22008	0.22	0.2508	0.25	RANDOM	88.915

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]
-5.4		-1.37	4.18		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.455
r_dihedral_angle_3_deg	17.272
r_dihedral_angle_4_deg	15.595
r_long_range_B_refined	14.84
r_long_range_B_other	14.839
r_scangle_other	9.269
r_mcangle_it	7.874
r_mcangle_other	7.872
r_dihedral_angle_1_deg	6.777
r_scbond_it	5.919
r_scbond_other	5.918
r_mcbond_other	5.062
r_mcbond_it	5.061
r_angle_refined_deg	1.564
r_angle_other_deg	0.983
r_chiral_restr	0.086
r_bond_refined_d	0.011
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	3480
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	29

Software

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