3E5D

Crystal structure of a putative glyoxalase i (lmof2365_0426) from listeria monocytogenes str. 4b f2365 at 2.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	1.1M sodium citrate, 0.15M sodium chloride, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
5.42	77.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.59	α = 90
b = 123.59	β = 90
c = 123.59	γ = 90

Symmetry
Space Group	I 21 3

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	Flat mirror (vertical focusing)	2008-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.7	29.136	99.7	0.051	22.2			8775		-3	103.91

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	2.7	2.8	98.8		0.991	2.2

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	SAD	THROUGHOUT	2.7	29.136	8766	416	99.8	0.173	0.172	0.198	RANDOM	57.474

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.224
r_dihedral_angle_4_deg	19.148
r_dihedral_angle_3_deg	12.377
r_scangle_it	5.127
r_dihedral_angle_1_deg	4.031
r_scbond_it	3.973
r_mcangle_it	2.134
r_angle_refined_deg	1.657
r_mcbond_it	1.373
r_angle_other_deg	0.959
r_xyhbond_nbd_refined	0.376
r_mcbond_other	0.243
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.216
r_symmetry_vdw_other	0.206
r_nbtor_refined	0.188
r_nbd_other	0.185
r_symmetry_vdw_refined	0.147
r_chiral_restr	0.095
r_nbtor_other	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	996
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing