1KO5

Crystal structure of gluconate kinase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	277	PEG6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.274	α = 90
b = 89.206	β = 105.14
c = 51.479	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MARRESEARCH		2001-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.845	EMBL/DESY, HAMBURG	BW7B

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	2.3	25	96.6	0.049	27.8	3	17024	17024			31.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.34	98.6		0.254	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.28	50	15607	15607	789	95.51	0.21665	0.21665	0.21356	0.27657	RANDOM	31.153

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]
2.3		1.13	0.26		-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.595
r_dihedral_angle_1_deg	3.735
r_scangle_it	3.241
r_scbond_it	1.933
r_angle_refined_deg	1.54
r_mcangle_it	1.295
r_mcbond_it	0.686
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.253
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2702
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	64

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling