2NUY

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	30% PEG400, 0.1M HEPES, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.47	72.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.09	α = 90
b = 109.09	β = 90
c = 171.29	γ = 120

Symmetry
Space Group	P 31 2 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 4		2005-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	50	99.6	0.056	17.6	6.2		41289		-3	52.971

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	2.5	2.65	97.1		0.348	5.3	4.2	6379

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	native structure of KDGA	2.5	47.25	41249	2131	99.6	0.16	0.159	0.191	RANDOM	29.73

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]
3.58	1.79		3.58		-5.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.905
r_dihedral_angle_3_deg	10.846
r_dihedral_angle_4_deg	10.748
r_scangle_it	10.47
r_scbond_it	8.145
r_mcangle_it	4.228
r_mcbond_it	3.651
r_dihedral_angle_1_deg	3.059
r_angle_refined_deg	1.327
r_mcbond_other	1.138
r_angle_other_deg	0.846
r_nbd_refined	0.212
r_symmetry_vdw_other	0.197
r_nbtor_refined	0.184
r_nbd_other	0.179
r_symmetry_vdw_refined	0.154
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.091
r_nbtor_other	0.087
r_symmetry_metal_ion_refined	0.07
r_metal_ion_refined	0.06
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4598
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
XDS	data reduction
XSCALE	data scaling