3GBT | pdb_00003gbt

Crystal structure of gluconate kinase from Lactobacillus acidophilus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	291	0.1 M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-Butanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.638	α = 90
b = 96.008	β = 93.32
c = 72.94	γ = 90

Symmetry
Space Group	C 1 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	110	CCD	ADSC QUANTUM 210	mirrors	2009-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9792	NSLS	X12C

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	2.4	50	97.1	0.146	11.2	5.8	33281	33170			34.76

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	2.4	2.53	88.3		0.606	1.7	4.5	4255

Refinement

Statistics
Diffraction ID	Structure Solution 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	SAD	2.4	40.079	33170	32163	1638	97.18	0.2009	0.1992	0.19	0.2306	0.22	Random	34.76

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]
-3.9761		-3.7951	11.2437		-7.2677

RMS Deviations
Key	Refinement Restraint Deviation
f_bond_d
f_bond_d_na
f_bond_d_prot
f_angle_d
f_angle_d_na
f_angle_d_prot
f_angle_deg
f_angle_deg_na
f_angle_deg_prot
f_dihedral_angle_d
f_dihedral_angle_d_na
f_dihedral_angle_d_prot
f_improper_angle_d
f_improper_angle_d_na
f_improper_angle_d_prot
f_mcbond_it
f_mcangle_it
f_scbond_it
f_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3801
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing