3T6C

Crystal structure of an enolase from pantoea ananatis (efi target efi-501676) with bound d-gluconate and mg

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GY1	PDB entry 3GY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	294	Protein (10 mM HEPES pH 7.8, 150 mM Nacl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (1 M K/Na Tartrate, 100 mM MES pH 6.0); Soak (1 M K/Na Tartrate, 100 mM MES pH 6.0, 20% ethylene glycol, 70 mM NaGluconate) 1 min, vapour diffusion, sitting drop, temperature 294K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.79	α = 90
b = 130.79	β = 90
c = 104.68	γ = 90

Symmetry
Space Group	P 4 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	98	CCD	RAYONIX MX225HE	mirrors	2011-06-25		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97930	APS	31-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	1.598	40	99	0.1	7.1	5.5	118520	118520

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	1.6	1.63	98.2		0.482		5.1	5789

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PDB entry 3GY1	1.598	21.223	110754	110754	1848	92.48	0.1396	0.1396	0.1391	0.1677	RANDOM	15.913

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]
-0.6241			-0.6241		0.854

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.477
f_angle_d	1.771
f_chiral_restr	0.138
f_bond_d	0.016
f_plane_restr	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6454
Nucleic Acid Atoms
Solvent Atoms	954
Heterogen Atoms	67

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.