4ACY | pdb_00004acy

Selenomethionine derivative of the GH99 endo-alpha-mannosidase from Bacteroides thetaiotaomicron

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		0.25 M NH4CL, 20% W/V PEG 3350, 0.1 M MES PH 6.5, 5 MM TCEP

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.721	α = 103.45
b = 60.002	β = 102.59
c = 78.666	γ = 98.59

Symmetry
Space Group	P 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	CCD	MARRESEARCH	MIRRORS	2009-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24

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	1.7	50	95.8	0.06	14.4	3.7		81218		2	19.2

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	1.7	1.76	91.8		0.48	4.9	3.5

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	SAD	THROUGHOUT	NONE	1.69	73.82	81218	4267	93.59	0.17676	0.17516	0.1779	0.20756	0.2094	RANDOM	21.241

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]
1.09	-1.09	0.55	-0.28	-0.42	-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.237
r_dihedral_angle_4_deg	15.481
r_dihedral_angle_3_deg	12.289
r_dihedral_angle_1_deg	5.876
r_angle_refined_deg	1.23
r_nbtor_refined	0.313
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.198
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.09
r_mcangle_it	0.016
r_bond_refined_d	0.01
r_mcbond_it	0.01
r_gen_planes_refined	0.008
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	5410
Nucleic Acid Atoms
Solvent Atoms	652
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing
ARP/wARP	phasing
REFMAC	refinement