2G8S | pdb_00002g8s

Crystal structure of the soluble Aldose sugar dehydrogenase (Asd) from Escherichia coli in the apo-form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.2	289	18 % PEG 6000, 100 mM CHES, 100 mM sodium chloride, 1 mM calcium chloride, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.829	α = 90
b = 113.475	β = 90.03
c = 75.372	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	100	CCD	ADSC QUANTUM 315		2004-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97935	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.315	75.378	72.2	0.057	0.057	6.9	3.3	162184	162184	0.2	5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.31	1.38	10.9	10.9	0.386	0.386	1.9	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	1.5	7.96	117547	117547	97142	94.15	0.149	0.148	0.149	0.1472	0.183	12.384

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.273
r_dihedral_angle_4_deg	15.992
r_dihedral_angle_3_deg	12.659
r_dihedral_angle_1_deg	6.184
r_sphericity_free	2.599
r_scangle_it	2.312
r_scbond_it	1.624
r_sphericity_bonded	1.595
r_angle_refined_deg	1.215
r_mcangle_it	1.125
r_rigid_bond_restr	0.927
r_mcbond_it	0.782
r_nbtor_refined	0.32
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.163
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.086
r_metal_ion_refined	0.047
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5963
Nucleic Acid Atoms
Solvent Atoms	1024
Heterogen Atoms	115

Software

Software
Software Name	Purpose
SCALA	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling