29MU | pdb_000029mu

Sesterterpene Synthase from Streptomyces mobaraensis (Sestermobaraene Synthase, SmTS1) in complex with pyrophosphate (PPi)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100 mM Tris, 0.15 M MgCl2, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.44	α = 90
b = 228.69	β = 90
c = 63.06	γ = 90

Symmetry
Space Group	P 21 21 2

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 EIGER X 16M		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	30	97.8	0.05	16.7	4.2		64377

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	98.8		0.667	2.1	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	30	61073	3214	97.73	0.22788	0.22657	0.2385	0.25194	0.2722	RANDOM	98.543

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]
-11.94			-9.82		21.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.302
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_4_deg	14.826
r_long_range_B_refined	5.216
r_long_range_B_other	5.131
r_dihedral_angle_1_deg	4.491
r_mcangle_it	1.851
r_mcangle_other	1.851
r_scangle_other	1.467
r_mcbond_it	1.366
r_mcbond_other	1.366
r_angle_refined_deg	1.143
r_angle_other_deg	1.029
r_scbond_it	1.016
r_scbond_other	1.015
r_rigid_bond_restr	0.736
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16171
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing