2YDP | pdb_00002ydp

Structure of the E242A mutant of the alpha-l-arabinofuranosidase arb93a from fusarium graminearum in complex with an iminosugar inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2W5N	PDB ENTRY 2W5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		20% PEG 8000, 100 MM SODIUM CACODYLATE PH 6.5, 200 MM LISO4, 20% GLYCEROL AS CYOPROTECTANT.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.93	α = 90.14
b = 57.8	β = 93.55
c = 91.6	γ = 114.5

Symmetry
Space Group	P 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	CCD	ADSC CCD		2009-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.85	35.47	95.2	0.1	5.5	2		86184		1.8

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	1.85	1.95	95.2		0.37	1.8	2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2W5N	1.85	33.97	81852	4325	95.2	0.174	0.171	0.17	0.226	0.23	RANDOM	21.56

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]
-0.27	-1.25	-0.26	0.28	-0.5	-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.626
r_dihedral_angle_4_deg	14.387
r_dihedral_angle_3_deg	14.166
r_dihedral_angle_1_deg	6.984
r_scangle_it	3.169
r_scbond_it	2.047
r_angle_refined_deg	1.528
r_mcangle_it	1.31
r_mcbond_it	0.76
r_nbtor_refined	0.314
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.135
r_metal_ion_refined	0.113
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8550
Nucleic Acid Atoms
Solvent Atoms	964
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing