4ONV

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	6.5	298	15%PEG 3350, 100mM Hepes pH 6.5, 200mM MgCl2, Microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.17	α = 90
b = 155.41	β = 90
c = 55.51	γ = 90

Symmetry
Space Group	P 21 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	100	CCD			2012-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.974	ESRF	BM14

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	1.99	19.79	98.6	0.405	4.81			83685		-3

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	1.99	2.04	91.2		0.035	0.44

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.57	19.79	37422	1970	98.91	0.24848	0.24658	0.2845	RANDOM	22.637

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]
-2.83			4.22		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.236
r_dihedral_angle_4_deg	22.325
r_dihedral_angle_3_deg	15.102
r_dihedral_angle_1_deg	6.004
r_mcangle_it	1.965
r_angle_refined_deg	1.476
r_scbond_it	1.316
r_mcbond_it	1.229
r_mcbond_other	1.228
r_angle_other_deg	1.186
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.004
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9037
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	182

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction