2NQL

Crystal structure of a member of the enolase superfamily from Agrobacterium tumefaciens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GL5	PDB entry 2GL5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	100MM SODIUM CACODYLATE, PH 6.5, 2M AMMONIUM SULFATE, 100MM NACL, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.071	α = 90
b = 102.071	β = 90
c = 369.202	γ = 120

Symmetry
Space Group	P 65 2 2

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 315	MIRRORS	2006-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.072	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	50	99.8	0.068	0.064	11.7	6.2	106184	106184

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	99		0.46	0.41	2.4	3.8	10308

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	THROUGHOUT	PDB entry 2GL5	1.8	20	-5	102915	102915	3183	99.72	0.17036	0.17036	0.16937	0.20144	RANDOM	27.165

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]
0.4	0.2		0.4		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.876
r_dihedral_angle_4_deg	15.174
r_dihedral_angle_3_deg	14.573
r_scangle_it	8.432
r_dihedral_angle_1_deg	6.96
r_scbond_it	5.861
r_mcangle_it	4.247
r_mcbond_it	3.319
r_angle_refined_deg	1.361
r_nbtor_refined	0.301
r_metal_ion_refined	0.256
r_symmetry_hbond_refined	0.244
r_chiral_restr	0.196
r_nbd_refined	0.179
r_xyhbond_nbd_refined	0.176
r_symmetry_vdw_refined	0.144
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5968
Nucleic Acid Atoms
Solvent Atoms	895
Heterogen Atoms	111

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
ADSC	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing