4OE7

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V8Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	6.5	298	100mM HEPES pH 6.5, 200mM Magnesium chloride, 15% PEG 3350, MICROBATCH UNDER OIL, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.24	α = 90
b = 155.14	β = 90
c = 55.58	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	0.97625	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	8.89	98.2	14.43	4.1		83414

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.04	87		2.76	3.42

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2V8Z	1.99	49.06	83414	79242	4171	98.27	0.1998	0.19804	0.23308	RANDOM	19.011

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]
-1.33			1.1		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.378
r_dihedral_angle_4_deg	21.045
r_dihedral_angle_3_deg	12.478
r_dihedral_angle_1_deg	6.229
r_long_range_B_other	4.106
r_long_range_B_refined	4.105
r_scangle_other	3.191
r_scbond_other	2.19
r_scbond_it	2.161
r_mcangle_it	1.946
r_mcangle_other	1.943
r_angle_refined_deg	1.896
r_mcbond_it	1.436
r_mcbond_other	1.435
r_angle_other_deg	1.356
r_chiral_restr	0.127
r_bond_refined_d	0.021
r_bond_other_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
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
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	205
Heterogen Atoms	192

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling