4V28 | pdb_00004v28

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with Man-Man-Methylumbelliferone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AD1	PDB ENTRY 4AD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.4		2.8 M SODIUM ACETATE PH 6.4

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.472	α = 90
b = 108.472	β = 90
c = 67.803	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		2013-04-19	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	1.2	39.5	99.9	0.06	12.6	6.2		122416		-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	1.2	1.22	99.4		0.46	2.3	3.2

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	PDB ENTRY 4AD1	1.2	76.7	116080	6135	99.79	0.10691	0.10584	0.12	0.12707	0.14	RANDOM	16.542

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]
0.06			0.06		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.318
r_dihedral_angle_2_deg	35.948
r_dihedral_angle_4_deg	15.874
r_dihedral_angle_3_deg	12.201
r_sphericity_bonded	9.948
r_dihedral_angle_1_deg	6.187
r_scangle_it	2.488
r_rigid_bond_restr	2.207
r_scbond_it	2.087
r_mcangle_it	1.662
r_angle_refined_deg	1.478
r_mcbond_it	1.29
r_mcbond_other	1.274
r_angle_other_deg	1.108
r_symmetry_vdw_refined	0.336
r_nbd_refined	0.289
r_symmetry_vdw_other	0.221
r_nbd_other	0.211
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.144
r_xyhbond_nbd_other	0.106
r_chiral_restr	0.092
r_nbtor_other	0.089
r_symmetry_hbond_refined	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.002
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	2807
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms	51

Software

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