5NE5 | pdb_00005ne5

Crystal structure of family 47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with kifunensine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 22% (w/v) polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.923	α = 90
b = 144.923	β = 90
c = 50.593	γ = 120

Symmetry
Space Group	H 3

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	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.05	36.23	99.2	0.09	1	7	4.7		183579

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.07	99.6		0.88	0.53	1.1	3.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.05	36.23	183575	9277	99.2	0.146	0.1456	0.15	0.1523	0.15	RANDOM	11.7418

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.574
r_dihedral_angle_4_deg	18.668
r_dihedral_angle_3_deg	12.023
r_dihedral_angle_1_deg	6.275
r_angle_other_deg	3.671
r_angle_refined_deg	1.872
r_mcangle_it	1.631
r_mcbond_it	1.166
r_mcbond_other	1.134
r_chiral_restr	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.574
r_dihedral_angle_4_deg	18.668
r_dihedral_angle_3_deg	12.023
r_dihedral_angle_1_deg	6.275
r_angle_other_deg	3.671
r_angle_refined_deg	1.872
r_mcangle_it	1.631
r_mcbond_it	1.166
r_mcbond_other	1.134
r_chiral_restr	0.119
r_bond_refined_d	0.021
r_gen_planes_other	0.02
r_gen_planes_refined	0.013
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3427
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	33

Software

Software
Software Name	Purpose
xia2	data reduction
Aimless	data scaling
REFMAC	refinement

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.