5M7Y

Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannotriose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	200 mM MgCl2, 100 mM HEPES pH7.0, 27% polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.414	α = 90
b = 44.016	β = 96.59
c = 85.079	γ = 90

Symmetry
Space Group	P 1 21 1

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-F		2016-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.980	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.55	51.82	99.8	0.035	1	21.8	4.1		263043

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	99.8		0.4	0.9	3.1	3.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.55	51.82	64689	3291	99.69	0.1487	0.147	0.1801	RANDOM	22.9027

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]
2.47		-0.19	-0.73		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.908
r_dihedral_angle_4_deg	17.234
r_dihedral_angle_3_deg	12.732
r_dihedral_angle_1_deg	6.345
r_angle_other_deg	3.65
r_mcangle_it	2.432
r_angle_refined_deg	2.067
r_mcbond_it	1.836
r_mcbond_other	1.836
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.908
r_dihedral_angle_4_deg	17.234
r_dihedral_angle_3_deg	12.732
r_dihedral_angle_1_deg	6.345
r_angle_other_deg	3.65
r_mcangle_it	2.432
r_angle_refined_deg	2.067
r_mcbond_it	1.836
r_mcbond_other	1.836
r_chiral_restr	0.128
r_gen_planes_other	0.026
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3479
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.