6BFY | pdb_00006bfy

Crystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FYM	PDB entry 2FYM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	2.0 M ammonium sulfate, 0.1 M MES, pH 6.0, 0.1 M sodium/potassium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.94	α = 90
b = 142.4	β = 90
c = 206.64	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD	Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror	2017-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.1949	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.81	78.61	100	0.116	0.132	0.062	0.991	6.1	4		283200			17.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.84	99.9		0.607	0.702	0.349	0.813	1.5	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB entry 2FYM	1.81	78.61	269041	14046	99.92	0.16892	0.16562	0.19	0.23223	0.23	RANDOM	26.19

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]
1.68			0.92		-2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.855
r_dihedral_angle_4_deg	17.431
r_sphericity_free	17.339
r_dihedral_angle_3_deg	14.479
r_sphericity_bonded	10.21
r_dihedral_angle_1_deg	6.915
r_scangle_other	5.124
r_scbond_it	4.763
r_scbond_other	4.758
r_long_range_B_refined	4.631
r_long_range_B_other	4.631
r_rigid_bond_restr	4.544
r_mcangle_it	3.938
r_mcangle_other	3.938
r_mcbond_it	3.563
r_mcbond_other	3.562
r_angle_refined_deg	2.231
r_angle_other_deg	1.18
r_chiral_restr	0.148
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19500
Nucleic Acid Atoms
Solvent Atoms	1103
Heterogen Atoms	206

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing