7PJD

The X-ray structure of juvenile hormone diol kinase from the silk worm Bombyx mori.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	Protein concentration: 10mg/ml in 0.1 M Bis-Tris pH 5.5 with 25 % (v/v) PEG 3350 as precipitant. The protein was dialysed against 1mM Ca2+ in phosphate-buffered saline before crystallisation.

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.64	α = 90
b = 79.43	β = 91.6
c = 100.93	γ = 90

Symmetry
Space Group	P 1 21 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 6M		2017-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.99	50.59	99.9	0.108	0.117	0.045	0.999	10.8	6.8		71164			32.4

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	1.99	2.04	99.9		1.593	1.722	0.65	0.645		6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5f6t, 4ndd	1.99	50.5	67669	3471	99.93	0.1932	0.1904	0.2476	RANDOM	41.702

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]
0.33		0.73	0.78		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.741
r_dihedral_angle_4_deg	24.033
r_dihedral_angle_3_deg	16.19
r_dihedral_angle_1_deg	6.122
r_angle_refined_deg	1.704
r_angle_other_deg	1.429
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.741
r_dihedral_angle_4_deg	24.033
r_dihedral_angle_3_deg	16.19
r_dihedral_angle_1_deg	6.122
r_angle_refined_deg	1.704
r_angle_other_deg	1.429
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8733
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
MrBUMP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.