6T75

Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzyme intermediate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T50

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.155	α = 91.977
b = 104.873	β = 97.733
c = 171.627	γ = 107.161

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		2019-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	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	2.55	99.9	98.7	0.994	6.1	3.6		148606

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	2.55	2.59			0.458	1

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	6T50	2.55	89.337	148575	7529	98.643	0.215	0.2138	0.2452	49.969

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]
2.778	-0.942	-0.34	-0.228	0.413	-1.823

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.326
r_dihedral_angle_4_deg	19.419
r_dihedral_angle_3_deg	17.894
r_dihedral_angle_1_deg	7.575
r_lrange_it	5.741
r_lrange_other	5.741
r_scangle_it	4.045
r_scangle_other	4.045
r_mcangle_it	3.862
r_mcangle_other	3.861
r_scbond_it	2.468
r_scbond_other	2.467
r_mcbond_it	2.437
r_mcbond_other	2.436
r_angle_refined_deg	1.548
r_angle_other_deg	1.255
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_other	0.241
r_nbd_refined	0.195
r_symmetry_nbd_other	0.177
r_symmetry_nbd_refined	0.171
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_14	0.074
r_ncsr_local_group_1	0.073
r_ncsr_local_group_11	0.072
r_ncsr_local_group_12	0.072
r_ncsr_local_group_13	0.072
r_ncsr_local_group_2	0.071
r_ncsr_local_group_5	0.071
r_ncsr_local_group_6	0.071
r_ncsr_local_group_7	0.071
r_ncsr_local_group_8	0.071
r_ncsr_local_group_10	0.071
r_ncsr_local_group_15	0.071
r_ncsr_local_group_3	0.07
r_ncsr_local_group_9	0.07
r_chiral_restr	0.068
r_ncsr_local_group_4	0.068
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31388
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	72

Software

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