2FYM | pdb_00002fym

Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E9I	Enolase structure 1E9I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2	VAPOR DIFFUSION, HANGING DROP	8.2	298	40% MPEG 550, 0.1M HEPES, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
3	VAPOR DIFFUSION, HANGING DROP	6	298	8% PEG 4K, 0.2 M imidazole maleate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
4	VAPOR DIFFUSION, HANGING DROP	7.5	298	27% PEG 600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.054	α = 90
b = 124.201	β = 90.58
c = 96.076	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	ADSC QUANTUM 315r		2004-05-08	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2004-02-24	M	SINGLE WAVELENGTH
3	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2004-03-09	M	SINGLE WAVELENGTH
4	1	x-ray	100	CCD	ADSC QUANTUM 4		2004-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0	ESRF	ID14-4
2	SYNCHROTRON	ESRF BEAMLINE ID29	0.9782	ESRF	ID29
3	ROTATING ANODE	RIGAKU	1.54
4	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0	ESRF	ID14-4

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
1,2,3,4	1.6	20	91.1	0.034	13.7	10.3	216453	216432	2	2

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)
	1.6	1.63	94.3		0.253	2.45	16.51

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	Enolase structure 1E9I	1.6	19.99	216453	205585	10847	90.92	0.16652	0.16472	0.16	0.20102	0.2	RANDOM	20.671

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]
-0.02		-0.01	-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.267
r_dihedral_angle_4_deg	18.674
r_dihedral_angle_3_deg	12.064
r_dihedral_angle_1_deg	5.413
r_sphericity_free	3.556
r_scangle_it	3.078
r_sphericity_bonded	2.843
r_scbond_it	2.697
r_rigid_bond_restr	2.495
r_mcangle_it	1.237
r_angle_refined_deg	1.157
r_mcbond_it	0.844
r_nbtor_refined	0.302
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.171
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12873
Nucleic Acid Atoms
Solvent Atoms	1930
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction