11TN | pdb_000011tn

Candida glabrata Glycogen Debranching Enzyme (GDE) in complex with Miglustat

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	0.1 M MES (pH 7), 7% v/v Tacsimate (pH 7), 20% w/v PEG MME 5K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.078	α = 90
b = 199.274	β = 90
c = 254.213	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS EIGER X 9M		2024-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	1	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.2	127.106	93.5	0.98	6.2	14.2		64558			60.61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.236	3.595			0.527

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 (All)	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	3.236	127.106	36605	1857	56.69	0.237	0.2354	0.2407	0.2735	0.2773	RANDOM	86.576

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]
-6.919			2.002		4.916

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.037
r_dihedral_angle_6_deg	11.683
r_lrange_it	7.84
r_lrange_other	7.84
r_dihedral_angle_1_deg	6.213
r_mcangle_other	3.392
r_mcangle_it	3.391
r_dihedral_angle_2_deg	3.233
r_scangle_it	2.999
r_scangle_other	2.999
r_mcbond_it	1.921
r_mcbond_other	1.92
r_scbond_it	1.617
r_scbond_other	1.617
r_angle_refined_deg	0.858
r_angle_other_deg	0.333
r_nbd_refined	0.187
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.142
r_xyhbond_nbd_refined	0.13
r_ncsr_local_group_1	0.125
r_symmetry_xyhbond_nbd_other	0.124
r_nbd_other	0.101
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.044
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23443
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing