7OP7 | pdb_00007op7

Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured N-alkyl cyclophellitol aziridine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JE8	2JE8.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	PEG 3350, sodium bromide, MES buffer

Crystal Properties
Matthews coefficient	Solvent content
2.41	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.761	α = 90
b = 114.707	β = 112.89
c = 98.639	γ = 90

Symmetry
Space Group	P 1 21 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		2021-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97629	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.85	67.66	99.9	0.053	0.997	8.3	5.5		158303

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	99.8		1.004	0.5	0.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2JE8.pdb	1.85	67.66	150387	7873	99.89	0.1918	0.1891	0.2	0.2436	0.25	RANDOM	32.299

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]
-2.52		-0.86	-0.19		2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.813
r_dihedral_angle_4_deg	20.647
r_dihedral_angle_3_deg	15.624
r_dihedral_angle_1_deg	7.889
r_angle_refined_deg	1.881
r_angle_other_deg	1.441
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.813
r_dihedral_angle_4_deg	20.647
r_dihedral_angle_3_deg	15.624
r_dihedral_angle_1_deg	7.889
r_angle_refined_deg	1.881
r_angle_other_deg	1.441
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13533
Nucleic Acid Atoms
Solvent Atoms	828
Heterogen Atoms	181

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.