3DAS | pdb_00003das

Structure of the PQQ-bound form of Aldose Sugar Dehydrogenase (Adh) from Streptomyces coelicolor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	0.1M HEPES, 20% PEG 6000, 0.1M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.033	α = 90
b = 41.26	β = 93.58
c = 85.931	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9184	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	50	95.2			43328	43328

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	1.6	48.91	2	41068	2249	94.89	0.13378	0.13238	0.1315	0.15939	0.1578	RANDOM	10.734

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]
-0.03		-0.05	0.31		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.28
r_dihedral_angle_4_deg	18.794
r_dihedral_angle_3_deg	10.634
r_dihedral_angle_1_deg	6.036
r_sphericity_free	2.455
r_scangle_it	2.086
r_sphericity_bonded	1.442
r_scbond_it	1.434
r_angle_refined_deg	1.28
r_mcangle_it	0.956
r_rigid_bond_restr	0.816
r_mcbond_it	0.646
r_nbtor_refined	0.309
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.174
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.083
r_metal_ion_refined	0.039
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
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_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2771
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing