5JKE | pdb_00005jke

Crystal structure of human IZUMO1-JUNO complex (crystal form 3)

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	20% PEG4000, 0.2 M Li2SO4, 0.1 M MES-NaOH pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.182	α = 90
b = 141.776	β = 90
c = 144.861	γ = 90

Symmetry
Space Group	P 2 21 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		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	2.86	48.3	100	28.5	13.2		31399

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	2.86	48.3	29880	1468	99.96	0.20429	0.20265	0.21	0.23817	0.24	RANDOM	86.849

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]
1.84			-1.49		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.872
r_dihedral_angle_4_deg	21.38
r_dihedral_angle_3_deg	17.46
r_long_range_B_refined	13.534
r_long_range_B_other	13.534
r_scangle_other	9.767
r_mcangle_other	8.501
r_mcangle_it	8.499
r_dihedral_angle_1_deg	6.593
r_scbond_it	6.483
r_scbond_other	6.483
r_mcbond_it	5.682
r_mcbond_other	5.676
r_angle_refined_deg	1.592
r_angle_other_deg	1.132
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004
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	6994
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	68

Software

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