9EQQ | pdb_00009eqq

Uhgb_MS mannoside synthase from an unknown human gut bacterium in complex with Mannose

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		285	0.2 M Calcium acetate, 0.1 M Imidazole pH 8.0, 20 %PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
4.8	74.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.629	α = 90
b = 176.629	β = 90
c = 83.539	γ = 120

Symmetry
Space Group	P 61 2 2

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 EIGER X 16M		2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.978565	SOLEIL	PROXIMA 1

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	2.55	47.586	100	0.102	4.8	40.3		1030781

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	2.55	2.69			0.718

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	2.55	47.586	25524	1278	99.969	0.181	0.1795	0.1871	0.2067	0.2078	59.848

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]
0.041	0.021		0.041		-0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.744
r_dihedral_angle_3_deg	13.441
r_lrange_other	9.575
r_lrange_it	9.56
r_dihedral_angle_1_deg	7.675
r_scangle_it	7.558
r_scangle_other	7.556
r_mcangle_it	6.45
r_mcangle_other	6.449
r_dihedral_angle_2_deg	6.089
r_scbond_it	4.936
r_scbond_other	4.934
r_mcbond_it	4.54
r_mcbond_other	4.537
r_angle_refined_deg	1.392
r_angle_other_deg	0.48
r_symmetry_nbd_other	0.191
r_nbd_refined	0.185
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.154
r_nbd_other	0.131
r_symmetry_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.085
r_symmetry_nbd_refined	0.084
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.032
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2733
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	16

Software

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