6ZJ6

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	3 M sodium acetate pH 6.6 - 7,4

Crystal Properties
Matthews coefficient	Solvent content
2.23	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.981	α = 90
b = 107.981	β = 90
c = 67.282	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-F		2011-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97630	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.09	76.35	95.9	0.059	0.065	0.027	0.997	12.5	5.1		153951			11.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.09	1.11	66.4		1.12	1.342	0.715	0.358	0.9	2.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6HMG	1.09	76.35	153946	7638	95.856	0.114	0.1133	0.1355	17.312

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]
0.098			0.098		-0.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.842
r_dihedral_angle_4_deg	16.775
r_dihedral_angle_3_deg	12.482
r_dihedral_angle_1_deg	6.652
r_rigid_bond_restr	4.737
r_lrange_it	4.268
r_scbond_it	4.24
r_scbond_other	4.24
r_scangle_it	4.118
r_scangle_other	4.118
r_lrange_other	3.929
r_mcangle_other	2.864
r_mcangle_it	2.855
r_mcbond_it	2.352
r_mcbond_other	2.351
r_angle_refined_deg	1.93
r_angle_other_deg	1.566
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.227
r_symmetry_nbd_other	0.195
r_nbd_other	0.194
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.12
r_symmetry_nbtor_other	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2906
Nucleic Acid Atoms
Solvent Atoms	463
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing