4UTF

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine and alpha- 1,2-mannobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PREVIOUSLY SOLVED NATIVE APO STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.6		2.8 M SODIUM ACETATE, PH 6.6

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.469	α = 90
b = 108.469	β = 90
c = 67.755	γ = 90

Symmetry
Space Group	I 4

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		2013-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.3	39.4	100	0.04	18.8	6.6		96371		-3.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	100		0.93	1.8	6.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PREVIOUSLY SOLVED NATIVE APO STRUCTURE	1.3	76.7	91564	4797	99.96	0.11333	0.11196	0.13	0.13901	0.15	RANDOM	19.787

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]
0.14			0.14		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.562
r_dihedral_angle_2_deg	36.055
r_dihedral_angle_4_deg	15.771
r_dihedral_angle_3_deg	13.299
r_sphericity_bonded	9.582
r_dihedral_angle_1_deg	6.303
r_mcangle_it	2.7
r_scangle_it	2.656
r_rigid_bond_restr	2.423
r_scbond_it	2.375
r_mcbond_it	2.146
r_mcbond_other	2.146
r_angle_refined_deg	1.517
r_angle_other_deg	1.221
r_symmetry_vdw_refined	0.354
r_nbd_refined	0.251
r_symmetry_vdw_other	0.2
r_nbd_other	0.19
r_nbtor_refined	0.189
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.093
r_xyhbond_nbd_other	0.086
r_nbtor_other	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2815
Nucleic Acid Atoms
Solvent Atoms	497
Heterogen Atoms	52

Software

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