7VEO | pdb_00007veo

Crystal structure of juvenile hormone acid methyltransferase silkworm JHAMT isoform3 complex with S-Adenosyl-L-homocysteine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7V2S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.15M DL-malic acid pH 7.0, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.15	α = 90
b = 69.17	β = 99.98
c = 57.82	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 PILATUS3 6M		2018-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9792	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.53	56.956	96.6	0.083	0.096	11.9	6.9		18812

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.53	2.6			0.856	0.524	2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7V2S	2.53	56.956	18811	904	96.314	0.195	0.192	0.1933	0.2414	0.2405	74.103

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]
-0.015			-0.041		0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.277
r_dihedral_angle_3_deg	18.134
r_lrange_it	12.817
r_lrange_other	12.816
r_dihedral_angle_4_deg	12.492
r_scangle_it	10.123
r_scangle_other	10.121
r_mcangle_other	7.798
r_mcangle_it	7.797
r_dihedral_angle_1_deg	7.575
r_scbond_it	6.661
r_scbond_other	6.66
r_mcbond_it	5.401
r_mcbond_other	5.387
r_angle_other_deg	2.261
r_angle_refined_deg	1.492
r_nbd_other	0.255
r_symmetry_xyhbond_nbd_refined	0.235
r_symmetry_nbd_other	0.221
r_nbd_refined	0.202
r_symmetry_nbd_refined	0.193
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.156
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.065
r_bond_other_d	0.034
r_gen_planes_other	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_symmetry_xyhbond_nbd_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4188
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing