8QCW

The crystal structure of the truncated form of Lotus japonicus kinase 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	27 mM NaNO3, 27 mM Na2HPO4, 27 mM ammonium sulfate, 0.1 M MES, 12% (v/v) PEG 500 MME & 6% (v/v) PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.318	α = 90
b = 69.323	β = 90
c = 99.641	γ = 90

Symmetry
Space Group	P 21 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 6M		2021-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.9	43.24	99.3	0.2	0.948	3.7	3		8837		-3	50

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.08	99.7		0.359	1.4	2.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.9	43.24	7936	882	98.76	0.2502	0.24367	0.3104	RANDOM	56.633

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]
-0.03			0.09		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.817
r_long_range_B_refined	7.899
r_long_range_B_other	7.898
r_dihedral_angle_1_deg	6.884
r_dihedral_angle_2_deg	6.228
r_mcangle_it	3.701
r_mcangle_other	3.7
r_scangle_other	2.935
r_mcbond_it	2.112
r_mcbond_other	2.112
r_scbond_it	1.635
r_scbond_other	1.608
r_angle_refined_deg	0.828
r_angle_other_deg	0.274
r_chiral_restr	0.048
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	2878
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing