6T6G

Bacteroides salyersiae GH164 beta-mannosidase in complex with noeuromycin

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	7	293	0.1 M ammonium tartrate pH 7.0, 13 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.754	α = 92.602
b = 105.096	β = 97.209
c = 170.544	γ = 105.096

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 PILATUS 6M-F		2019-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.916	Diamond	I04-1

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	2.06	101.13	98.3	0.986	5.2	3.5		280992

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	2.06	2.1			0.6

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	2.06	90.191	280985	13971	98.228	0.214	0.2122	0.2399	44.862

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]
1.755	0.496	-0.979	-0.093	0.21	-1.595

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.764
r_dihedral_angle_4_deg	24.434
r_dihedral_angle_3_deg	16.356
r_dihedral_angle_1_deg	7.739
r_lrange_it	5.166
r_lrange_other	5.158
r_scangle_it	3.123
r_scangle_other	3.123
r_mcangle_it	2.875
r_mcangle_other	2.875
r_scbond_it	1.879
r_scbond_other	1.879
r_mcbond_it	1.799
r_mcbond_other	1.799
r_angle_refined_deg	1.613
r_angle_other_deg	1.368
r_nbd_other	0.239
r_nbd_refined	0.204
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.148
r_symmetry_nbd_refined	0.125
r_chiral_restr_other	0.081
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.08
r_ncsr_local_group_10	0.079
r_ncsr_local_group_4	0.078
r_ncsr_local_group_13	0.075
r_ncsr_local_group_14	0.075
r_ncsr_local_group_2	0.074
r_ncsr_local_group_8	0.074
r_ncsr_local_group_1	0.073
r_ncsr_local_group_3	0.073
r_ncsr_local_group_5	0.073
r_ncsr_local_group_9	0.073
r_ncsr_local_group_12	0.073
r_ncsr_local_group_15	0.073
r_ncsr_local_group_7	0.072
r_ncsr_local_group_6	0.071
r_ncsr_local_group_11	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31476
Nucleic Acid Atoms
Solvent Atoms	1029
Heterogen Atoms	96

Software

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