8DZD

Structure of MS3494 from Mycobacterium smegmatis bound to sucrose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	26 % PEG 4K, 0.2 M Lithium acetate (pH 7.5) Soaked in 20 % Sucrose

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.463	α = 90
b = 98.463	β = 90
c = 45.581	γ = 120

Symmetry
Space Group	P 6

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		2022-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.9	33.469	99.9	0.09	0.095	0.999	20.4	10.2		20058

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95			0.746	0.784	0.95	4.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7REF	1.901	33.469	20057	958	99.856	0.142	0.1404	0.175	23.013

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]
-1.309	-0.654		-1.309		4.246

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.418
r_dihedral_angle_3_deg	14.335
r_dihedral_angle_2_deg	10.643
r_lrange_it	6.385
r_lrange_other	6.337
r_dihedral_angle_1_deg	5.823
r_scangle_it	4.943
r_scangle_other	4.941
r_scbond_it	3.237
r_scbond_other	3.237
r_mcangle_it	2.829
r_mcangle_other	2.828
r_mcbond_it	1.927
r_mcbond_other	1.913
r_angle_refined_deg	1.472
r_angle_other_deg	0.546
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.211
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.186
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.158
r_ncsr_local_group_1	0.106
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2038
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing