8JPU | pdb_00008jpu

Crystal Structure of the acyltransferase domain from the fifth module of the tylosin polyketide synthase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M lithium sulfate, 0.1 M Tris pH 7.5, 29% PEG3350,VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.949	α = 90
b = 138.376	β = 90
c = 209.855	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 PILATUS3 6M		2021-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

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	2.5	50	78.2	0.109	0.118	0.043	0.996	5.5	6.1		52874

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	2.5	2.54	74.2		0.745	0.817	0.313	0.727		5.5

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	2.5	39.46	47448	2453	73.85	0.20526	0.20228	0.21	0.26301	0.26	RANDOM	53.829

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]
1.12			-1.3		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.31
r_long_range_B_refined	18.748
r_long_range_B_other	18.748
r_mcangle_it	9.864
r_mcangle_other	9.864
r_scangle_other	9.595
r_dihedral_angle_1_deg	7.572
r_mcbond_it	5.905
r_mcbond_other	5.905
r_dihedral_angle_2_deg	5.821
r_scbond_it	5.605
r_scbond_other	5.604
r_angle_refined_deg	0.834
r_angle_other_deg	0.291
r_chiral_restr	0.042
r_gen_planes_refined	0.009
r_bond_refined_d	0.003
r_gen_planes_other	0.001
r_bond_other_d
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	11950
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing