4AD5 | pdb_00004ad5

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin 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 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
2.33	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.844	α = 90
b = 108.844	β = 90
c = 67.762	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	120	IMAGE PLATE	MARRESEARCH	OSMICS MULTILAYER OPTICS	2011-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.9	40	100	0.06	19.5	6.1		31280		2	25.6

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	1.9	2	100		0.23	7.1	6

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 STRUCTURE OF CLOSELY RELATED HOMOLOG	1.9	39.53	25505	1360	85.73	0.16052	0.15813	0.16	0.2053	0.2	RANDOM	25.457

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]
0.38			0.38		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.193
r_dihedral_angle_4_deg	15.077
r_dihedral_angle_3_deg	14.848
r_dihedral_angle_1_deg	5.996
r_angle_refined_deg	1.207
r_mcangle_it	1.207
r_nbtor_refined	0.314
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.152
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_mcbond_it	0.011
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	2819
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	45

Software

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