5M1I

Structure of GH36 alpha-galactosidase from Thermotoga maritima in a covalent complex with a cyclopropyl carbasugar.

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M ammonium sulfate, 0.13 M ammonium citrate Protein was incubated with inhibitor at 333 K for 16 hours prior to crystallisation

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.903	α = 90
b = 96.239	β = 90
c = 97.589	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M-F		2015-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.55	68.52	100	0.068	12.6	6.5		92049

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	1.55	1.58	99.9		0.864	2	6.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5M0X	1.55	68.52	87347	4568	99.94	0.155	0.15357	0.18251	RANDOM	22.906

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]
2.79			-1.51		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.689
r_dihedral_angle_4_deg	17.937
r_dihedral_angle_3_deg	12.819
r_dihedral_angle_1_deg	6.661
r_long_range_B_refined	6.423
r_long_range_B_other	6.423
r_scangle_other	5.846
r_scbond_it	3.991
r_scbond_other	3.988
r_mcangle_it	2.459
r_mcangle_other	2.458
r_mcbond_it	1.821
r_mcbond_other	1.821
r_angle_refined_deg	1.68
r_angle_other_deg	0.826
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4349
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	90

Software

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