1KO8 | pdb_00001ko8

Crystal structure of gluconate kinase

X-RAY DIFFRACTION

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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
2.47	50.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.79	α = 90
b = 89.12	β = 109.69
c = 51.56	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	CCD	BRUKER SMART 1000		2001-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.093	MAX II	I711

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	2.4	48.8	99.4	0.094	4.5	4.1	14896	14896			51.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.53	99.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	25	14889	14889	773	98.07	0.25665	0.25386	0.2478	0.309	0.3028	RANDOM	51.127

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]
5.65		0.51	-0.31		-4.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.288
r_dihedral_angle_1_deg	3.967
r_scangle_it	3.195
r_scbond_it	2.009
r_angle_refined_deg	1.937
r_mcangle_it	1.385
r_mcbond_it	0.75
r_nbd_refined	0.294
r_xyhbond_nbd_refined	0.253
r_symmetry_vdw_refined	0.238
r_symmetry_hbond_refined	0.221
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2673
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	35

Software

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