2P1E

Crystal structure of the Leishmania infantum glyoxalase II with D-Lactate at the active site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	288	30% PEG 8K, 0.2M MgCl2, 0.1M ammonium acetate - soaked 30 min in 40% PEG 8K, 0.2M MgCl2, 0.1M ammonium acetate, 10mM S-D-lactoyltrypanothione, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.172	α = 90
b = 89.121	β = 90
c = 85.98	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315	Undulator	2006-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.9	53.642	100	0.087	0.087	5.1	13.8	20715	20715			24.4

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	1.9	2	100		0.488	0.488	1.5	14.1	2983

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2P18	1.9	53.61	20692	20692	1060	99.97	0.261	0.183	0.181	0.22	RANDOM	26.204

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]
-0.37			0.06		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.251
r_dihedral_angle_4_deg	17.365
r_dihedral_angle_3_deg	13.517
r_dihedral_angle_1_deg	8.724
r_scangle_it	3.139
r_scbond_it	2.242
r_angle_refined_deg	1.54
r_mcangle_it	1.22
r_mcbond_it	0.831
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.251
r_dihedral_angle_4_deg	17.365
r_dihedral_angle_3_deg	13.517
r_dihedral_angle_1_deg	8.724
r_scangle_it	3.139
r_scbond_it	2.242
r_angle_refined_deg	1.54
r_mcangle_it	1.22
r_mcbond_it	0.831
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.23
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.116
r_metal_ion_refined	0.024
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2129
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.