9ERH | pdb_00009erh

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with 1,2-beta-mannobiose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	285

Crystal Properties
Matthews coefficient	Solvent content
4.76	74.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.183	α = 90
b = 178.183	β = 90
c = 83.675	γ = 120

Symmetry
Space Group	P 61

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 PILATUS3 6M		2023-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

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	2.65	154.31	100	0.076	7.1	5.7		44200

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	2.65	2.79			0.752

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.65	50	44174	2184	99.937	0.17	0.1689	0.1809	0.1816	0.1907	71.379

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]
-3.916			-3.916		7.833

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.006
r_dihedral_angle_6_deg	8.43
r_dihedral_angle_1_deg	5.833
r_lrange_it	5.095
r_lrange_other	5.095
r_mcangle_it	3.312
r_mcangle_other	3.311
r_scangle_it	3.007
r_scangle_other	3.007
r_mcbond_it	1.898
r_mcbond_other	1.898
r_dihedral_angle_2_deg	1.87
r_scbond_it	1.679
r_scbond_other	1.679
r_angle_refined_deg	0.732
r_angle_other_deg	0.289
r_symmetry_nbd_refined	0.18
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.17
r_nbd_refined	0.148
r_nbd_other	0.128
r_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_refined	0.05
r_ncsr_local_group_1	0.037
r_chiral_restr	0.032
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5466
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	56

Software

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