2NUX

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure in p6522 at 2.5 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
4.25	71.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.509	α = 90
b = 109.509	β = 90
c = 319.559	γ = 120

Symmetry
Space Group	P 65 2 2

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 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	2.5	36	90.1	0.155	23.77	33.1		36273		-3	50.216

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	2.55	53		0.39	8	19.8	1194

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 2NUW	2.5	36	40218	36261	1878	90.16	0.177	0.175	0.216	RANDOM	28.345

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]
2.43	1.21		2.43		-3.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.77
r_dihedral_angle_3_deg	10.74
r_scangle_it	9.896
r_dihedral_angle_4_deg	9.534
r_scbond_it	7.784
r_mcangle_it	4.42
r_mcbond_it	3.684
r_dihedral_angle_1_deg	2.951
r_angle_refined_deg	1.34
r_mcbond_other	1.155
r_angle_other_deg	0.861
r_symmetry_vdw_other	0.25
r_nbd_refined	0.211
r_nbtor_refined	0.185
r_nbd_other	0.183
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.092
r_nbtor_other	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	94
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