7FE4 | pdb_00007fe4

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with glucose

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7FE3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	300 mM ammonium citrate, pH 7.0-8.0, 10 mM TCEP, 12% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.505	α = 90
b = 194.201	β = 116.598
c = 112.006	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 S 2M		2020-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.9795	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.4	50	98	0.06	0.065	0.025	0.999	15.6	6.8		451842

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	96.6		0.755	0.82	0.318	0.81	2.4	6.5

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	7FE3	1.4	44.704	451583	22421	97.986	0.157	0.1566	0.16	0.1702	0.18	25.135

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]
-0.073		0.105	0.162		-0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.912
r_dihedral_angle_4_deg	13.57
r_dihedral_angle_3_deg	13.065
r_dihedral_angle_1_deg	6.866
r_lrange_it	4.721
r_lrange_other	4.6
r_scangle_it	1.745
r_scangle_other	1.745
r_angle_refined_deg	1.526
r_angle_other_deg	1.454
r_scbond_it	1.131
r_scbond_other	1.131
r_mcangle_it	0.979
r_mcangle_other	0.979
r_mcbond_it	0.612
r_mcbond_other	0.612
r_symmetry_nbd_refined	0.321
r_nbd_refined	0.209
r_nbd_other	0.202
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.128
r_xyhbond_nbd_refined	0.112
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15741
Nucleic Acid Atoms
Solvent Atoms	1668
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building