2NUW

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution

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
4.45	72.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.16	α = 90
b = 108.16	β = 90
c = 171.852	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		2004-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	1.8	30	99.9	0.096	14.14	10.9		107995		-3	30.218

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	1.8	1.88	99.8		0.559	2.3	4	13009

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1w3n	1.8	29.35	108033	107995	5421	99.96	0.158	0.157	0.179	RANDOM	13.196

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]
2.18	1.09		2.18		-3.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.432
r_dihedral_angle_4_deg	12.683
r_scangle_it	11.714
r_dihedral_angle_3_deg	11.35
r_scbond_it	8.597
r_mcangle_it	4.454
r_mcbond_it	4.23
r_dihedral_angle_1_deg	3.898
r_angle_refined_deg	1.472
r_mcbond_other	1.28
r_angle_other_deg	0.891
r_nbd_refined	0.211
r_nbd_other	0.186
r_nbtor_refined	0.185
r_symmetry_vdw_other	0.174
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.143
r_symmetry_vdw_refined	0.103
r_chiral_restr	0.101
r_nbtor_other	0.09
r_metal_ion_refined	0.025
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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	410
Heterogen Atoms	1

Software

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