3EO3

Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	291	15% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 5.6, vapor diffusion, sitting drop, temperature 291K
2	VAPOR DIFFUSION, SITTING DROP	6	291	14.55% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 6.0, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.946	α = 90
b = 127.946	β = 90
c = 127.247	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	MARMOSAIC 300 mm CCD		2007-11-29	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315		2008-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97926	APS	23-ID-B
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.97921	APS	19-ID

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	2.84	30	100	0.089	12.9	11.1		29072

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	2.84	2.94	100		0.978		10.5	2860

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.84	30	28742	1071	99.653	0.207	0.205	0.245	THIN SHELLS (SFTOOLS)	24.804

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]
0.212	0.106		0.212		-0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.173
r_dihedral_angle_4_deg	15.853
r_dihedral_angle_3_deg	12.927
r_dihedral_angle_1_deg	4.387
r_scangle_it	1.559
r_mcangle_it	1.452
r_angle_refined_deg	1.131
r_scbond_it	0.942
r_angle_other_deg	0.868
r_mcbond_it	0.818
r_mcbond_other	0.114
r_chiral_restr	0.063
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5885
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling