7FE2

Crystal structure of the mutant E494Q of GH92 alpha-1,2-mannosidase from Enterococcus faecalis ATCC 10100 in complex with alpha-1,2-mannobiose

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
2.73	54.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.626	α = 90
b = 168.61	β = 90
c = 260.282	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		2021-06-27	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	1.75	50	99.6	0.141	0.147	0.04	0.998	12.2	13.3		354371

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	1.75	1.84	99.1		1.254	1.305	0.361	0.681	2.1	12.8

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	1.75	48.566	354296	17508	99.555	0.17	0.1686	0.1979	26

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]
-0.506			-0.339		0.845

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.741
r_dihedral_angle_4_deg	16.879
r_dihedral_angle_3_deg	14.244
r_dihedral_angle_1_deg	7.043
r_lrange_it	5.675
r_lrange_other	5.632
r_scangle_it	4.295
r_scangle_other	4.295
r_mcangle_it	2.968
r_mcangle_other	2.968
r_scbond_it	2.854
r_scbond_other	2.854
r_mcbond_it	2.084
r_mcbond_other	2.084
r_angle_refined_deg	1.612
r_angle_other_deg	1.411
r_nbd_refined	0.203
r_nbd_other	0.186
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.169
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.116
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.08
r_metal_ion_refined	0.078
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	1773
Heterogen Atoms	212

Software

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