6T7G

Bacteroides salyersiae GH164 beta-mannosidase in complex with mannoimidazole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T5O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	ammonium tartrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.71	α = 92.29
b = 104.743	β = 97.273
c = 170.568	γ = 106.301

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	PIXEL	DECTRIS EIGER2 X 16M		2019-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976230	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	168.66	100	0.998	6.9	2		424506

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83			0.666

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	6t5o	1.8	168.66	424505	21073	99.96	0.208	0.2065	0.2312	39.475

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]
2.236	1.593	0.199	0.068	0.686	-3.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.17
r_dihedral_angle_4_deg	18.975
r_dihedral_angle_3_deg	14.102
r_dihedral_angle_1_deg	7.219
r_lrange_it	6.999
r_lrange_other	6.99
r_scangle_it	5.821
r_scangle_other	5.821
r_mcangle_it	4.384
r_mcangle_other	4.384
r_scbond_it	4.005
r_scbond_other	4.005
r_mcbond_it	3.343
r_mcbond_other	3.342
r_angle_other_deg	2.31
r_angle_refined_deg	1.427
r_nbd_other	0.273
r_symmetry_nbd_refined	0.255
r_symmetry_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.203
r_nbd_refined	0.2
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.071
r_symmetry_nbtor_other	0.068
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.02
r_gen_planes_other	0.011
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31572
Nucleic Acid Atoms
Solvent Atoms	1666
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing