1KO4

Crystal structure of gluconate kinase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	PEG6000, LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.231	α = 90
b = 72.602	β = 90
c = 79.079	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MARRESEARCH		2000-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.97830	EMBL/DESY, Hamburg	BW7A

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	2.6	25	99.3	0.063	27.9	12.6	13617	13617			30.9

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)
	2.55	2.58	94.9		0.158	8.4

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	2.5	79.06	13603	13603	681	98.29	0.243	0.243	0.2399	0.30421	RANDOM	30.86

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]
-1.76			3.55		-1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.558
r_dihedral_angle_1_deg	4.103
r_scangle_it	4.041
r_scbond_it	2.428
r_angle_refined_deg	1.797
r_mcangle_it	1.695
r_mcbond_it	0.879
r_symmetry_hbond_refined	0.444
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.276
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.112
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2563
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	2

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling