2WSB

Crystal structure of the short-chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel		SWISS PROT MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		4% N-PROPANOLE, 100MM SODIUM CACODYLATE, PH 6.5, 200MM SODIUM ACETATE, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.71	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.79	α = 90
b = 106.62	β = 90
c = 109.33	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	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.25	19.94	98.6	0.1	8.4	6.7		313700		2	20.5

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	1.25	1.28	92.9		0.56	2	2.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SWISS PROT MODEL	1.25	19.94	313320	15666	99.88	0.13609	0.13393	0.17749	RANDOM	21.51

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]
0.09			-0.06		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.97
r_sphericity_free	21.107
r_dihedral_angle_4_deg	18.654
r_dihedral_angle_3_deg	12.454
r_sphericity_bonded	9.851
r_scangle_it	8.378
r_scbond_it	6.863
r_dihedral_angle_1_deg	6.314
r_mcangle_it	4.112
r_mcbond_it	3.1
r_rigid_bond_restr	3.07
r_angle_refined_deg	2.581
r_symmetry_vdw_refined	0.264
r_symmetry_hbond_refined	0.254
r_chiral_restr	0.168
r_bond_refined_d	0.03
r_gen_planes_refined	0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
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
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7392
Nucleic Acid Atoms
Solvent Atoms	1765
Heterogen Atoms	210

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing