7FE1

Crystal structure of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with methyl alpha-1,2-C-mannobioside

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	100 mM sodium citrate, pH 5.0-5.6, 100 mM magnesium acetate, 200 mM ammonium sulfate, 5% PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.162	α = 90
b = 169.601	β = 90
c = 258.659	γ = 90

Symmetry
Space Group	C 2 2 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 S 2M		2021-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.72	50	100	0.121	0.125	0.034	0.999	17.3	13.6		375878

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	1.72	1.81	100		1.168	1.214	0.327	0.759	2.5	13.5

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	6DWO	1.72	48.621	375801	18587	99.99	0.15	0.1489	0.1714	23.049

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]
-0.029			-0.022		0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.079
r_dihedral_angle_4_deg	17.515
r_dihedral_angle_3_deg	13.563
r_dihedral_angle_1_deg	6.889
r_lrange_it	5.832
r_lrange_other	5.704
r_scangle_it	4.84
r_scangle_other	4.84
r_scbond_it	3.278
r_scbond_other	3.278
r_mcangle_it	2.467
r_mcangle_other	2.467
r_mcbond_it	1.911
r_mcbond_other	1.911
r_angle_refined_deg	1.733
r_angle_other_deg	1.493
r_nbd_other	0.236
r_nbd_refined	0.207
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.169
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.069
r_metal_ion_refined	0.035
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23052
Nucleic Acid Atoms
Solvent Atoms	2760
Heterogen Atoms	184

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building