8B5M | pdb_00008b5m

Crystal structure of GH47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with cyclosulfamidate inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	23% PEG3350, 0.1 M MES pH 7.0, 0.2 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.134	α = 90
b = 144.134	β = 90
c = 50.32	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 EIGER2 XE 16M		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.799	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	0.97	72.07	100	0.155	0.05	0.999	7.7	10.2		230864

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.97	0.99	100		1.49	0.49	0.605	1.3	10

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4AYO	0.97	72.067	230864	11679	99.987	0.138	0.1373	0.15	0.148	0.16	7.642

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		0.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.543
r_dihedral_angle_4_deg	16.508
r_dihedral_angle_3_deg	11.651
r_dihedral_angle_1_deg	6.493
r_lrange_it	3.284
r_lrange_other	2.643
r_angle_refined_deg	1.919
r_scangle_it	1.759
r_scangle_other	1.758
r_angle_other_deg	1.698
r_scbond_it	1.238
r_scbond_other	1.237
r_mcangle_other	1.04
r_mcangle_it	1.038
r_mcbond_it	0.704
r_mcbond_other	0.698
r_nbd_refined	0.233
r_nbd_other	0.227
r_symmetry_nbd_refined	0.226
r_nbtor_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.182
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.089
r_metal_ion_refined	0.074
r_chiral_restr_other	0.052
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3446
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms	19

Software

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