31AO | pdb_000031ao

A. niger ManA in covalent complex with pseudotrisaccharide inhibitor

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		298	0.1 M Tris pH 7.8 2.2 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.04	α = 90
b = 68.226	β = 90
c = 73.32	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	100	PIXEL	DECTRIS EIGER X 4M		2026-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	1.419	30.95	99.9	0.988	4.6	5.9		64027

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	1.42	1.44			0.209		6

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.419	30.948	64027	3126	99.777	0.181	0.1802	0.1812	0.2009	0.201	12.695

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]
0.553			-0.419		-0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.224
r_dihedral_angle_3_deg	11.02
r_dihedral_angle_1_deg	6.154
r_dihedral_angle_2_deg	5.639
r_lrange_it	4.984
r_lrange_other	4.701
r_scangle_it	3.533
r_scangle_other	3.112
r_scbond_it	2.34
r_scbond_other	2.044
r_mcangle_other	1.986
r_mcangle_it	1.985
r_angle_refined_deg	1.692
r_mcbond_it	1.274
r_mcbond_other	1.274
r_angle_other_deg	0.608
r_nbd_other	0.249
r_nbd_refined	0.217
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.156
r_symmetry_nbd_refined	0.152
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2653
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing