9UN4 | pdb_00009un4

Crystal structure of juvenile hormone acid methyltransferase castaneum JHAMT3 from Tribolium castaneum

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7EBS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	0.1 M Bis-Tris pH 5.5, 0.2 M Sodium chloride, and 25% polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.269	45.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.597	α = 90
b = 71.476	β = 90
c = 133.984	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		2023-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97918	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	48.88	99.2	0.17	0.18	0.057	9.1	9.2		19950

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	99.8		0.927	0.977	0.301	2.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	48.88	19900	974	98.848	0.247	0.2449	0.2452	0.2945	0.2952	36.047

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]
-1.562			2.843		-1.281

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.969
r_dihedral_angle_4_deg	20.403
r_dihedral_angle_3_deg	16.544
r_lrange_it	7.548
r_lrange_other	7.548
r_dihedral_angle_1_deg	7.515
r_scangle_it	5.595
r_scangle_other	5.595
r_mcangle_it	4.198
r_mcangle_other	4.198
r_scbond_it	3.371
r_scbond_other	3.37
r_mcbond_it	2.623
r_mcbond_other	2.621
r_angle_other_deg	2.245
r_angle_refined_deg	1.523
r_symmetry_xyhbond_nbd_refined	0.403
r_symmetry_nbd_refined	0.379
r_nbd_other	0.341
r_symmetry_nbd_other	0.226
r_nbd_refined	0.199
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_other	0.103
r_chiral_restr	0.072
r_symmetry_nbtor_other	0.071
r_bond_other_d	0.034
r_gen_planes_other	0.008
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4301
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PROCOR	data scaling
MOLREP	phasing