4AD3

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with Glucose-1,3-deoxymannojirimycin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		0.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)

Crystal Properties
Matthews coefficient	Solvent content
3.52	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 222.478	α = 90
b = 222.478	β = 90
c = 84.715	γ = 120

Symmetry
Space Group	P 31 2 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	MIRRORS	2011-05-14	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	2	50	99.8	0.15	11.4	10.1		161771		2	26.2

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	2	2.11	98.5		0.98	2.4	9.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG	2	46.49	153609	8060	99.73	0.176	0.17464	0.20153	RANDOM	30.933

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]
0.12	0.06		0.12		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.237
r_dihedral_angle_4_deg	15.441
r_dihedral_angle_3_deg	14.586
r_dihedral_angle_1_deg	5.938
r_angle_refined_deg	1.242
r_mcangle_it	1.242
r_nbtor_refined	0.313
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_mcbond_it	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10965
Nucleic Acid Atoms
Solvent Atoms	1374
Heterogen Atoms	88

Software

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