7OP6 | pdb_00007op6

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	291	PEG 3350, sodium bromide, MES buffer

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.92	α = 90
b = 116.858	β = 114.15
c = 100.844	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 PILATUS 6M-F		2016-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	2.05	92.19	98.6	0.049	0.997	8.9	4.1		119933

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	2.05	2.09	97.9		0.522	0.535		4

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	2.05	92.19	113966	5938	98.47	0.1877	0.1854	0.19	0.2333	0.24	RANDOM	33.93

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]
-0.85		-0.1	-0.68		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.203
r_dihedral_angle_4_deg	17.925
r_dihedral_angle_3_deg	14.612
r_dihedral_angle_1_deg	7.482
r_angle_refined_deg	1.578
r_angle_other_deg	1.248
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.203
r_dihedral_angle_4_deg	17.925
r_dihedral_angle_3_deg	14.612
r_dihedral_angle_1_deg	7.482
r_angle_refined_deg	1.578
r_angle_other_deg	1.248
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13496
Nucleic Acid Atoms
Solvent Atoms	902
Heterogen Atoms	199

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.