6WNS | pdb_00006wns

The structure of a CoA-dependent acyl-homoserine lactone synthase, MesI

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5W8E	PDB entry 5W8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		282	0.1 M sodium cacodylate, pH 6.5, 40% v/v MPD, 5% w/v PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.673	α = 90
b = 65.673	β = 90
c = 113.539	γ = 90

Symmetry
Space Group	P 43 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	80	CCD	MARMOSAIC 300 mm CCD		2017-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.93	56.8	99.8	1	37.9	20		19634

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.93			0.842

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	PDB entry 5W8E	1.93	56.8	19633	986	99.746	0.216	0.2146	0.22	0.2348	0.24	66.755

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]
0.765			0.765		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.121
r_dihedral_angle_3_deg	17.746
r_dihedral_angle_4_deg	17.234
r_lrange_it	11.058
r_lrange_other	11.042
r_dihedral_angle_1_deg	7.637
r_scangle_it	5.211
r_scangle_other	5.209
r_mcangle_it	4.033
r_mcangle_other	4.031
r_scbond_it	3.492
r_scbond_other	3.49
r_mcbond_it	2.922
r_mcbond_other	2.921
r_angle_refined_deg	1.989
r_angle_other_deg	1.481
r_xyhbond_nbd_refined	0.29
r_symmetry_xyhbond_nbd_other	0.274
r_nbd_refined	0.268
r_nbd_other	0.26
r_symmetry_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.18
r_chiral_restr	0.098
r_symmetry_nbd_refined	0.095
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.014
r_xyhbond_nbd_other	0.013
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1558
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms

Software

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