8QIJ | pdb_00008qij

Crystallographic Structure of a Salicylate Synthase from M. abscessus (Mab-SaS)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	B1MAQ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	23-27% PEG 3350, 0.15-0.25M ammonium sulphate, 0.1M BIS-TRIS (pH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.34	α = 90
b = 94.76	β = 90
c = 102.46	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	Pt-coated cylindrical mirror	2022-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	2.07	56.1	100	0.186	0.195	0.057	0.997	11.9	11.4		56395

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	2.073	2.109	100		1.281	1.34	0.389	0.818	2.2	11.7

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	2.073	56.054	56394	2677	99.963	0.179	0.1769	0.19	0.2171	0.22	33.12

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]
1.933			-2.589		0.656

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.348
r_dihedral_angle_3_deg	14.157
r_dihedral_angle_1_deg	6.928
r_lrange_it	6.585
r_lrange_other	6.54
r_dihedral_angle_2_deg	5.81
r_scangle_it	4.758
r_scangle_other	4.721
r_mcangle_other	3.481
r_mcangle_it	3.478
r_scbond_it	2.969
r_scbond_other	2.936
r_mcbond_it	2.226
r_mcbond_other	2.223
r_angle_refined_deg	1.217
r_angle_other_deg	0.409
r_nbd_refined	0.201
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_other	0.149
r_nbd_other	0.14
r_symmetry_xyhbond_nbd_refined	0.113
r_symmetry_nbd_refined	0.104
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6636
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing