2P18 | pdb_00002p18

Crystal structure of the Leishmania infantum glyoxalase II

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QH3	PDB ENTRY 1QH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	288	30% PEG 4K, 0.2M MgCl2, 0.1M Ammonium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.705	α = 90
b = 88.989	β = 90
c = 85.864	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	1.8	53.376	99.8	0.069	0.069	6.5	5.7	23962	23962			22.4

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	1.8	1.9	100		0.468	0.468	1.6	5.8	3459

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QH3	1.8	53.38	23955	23955	1224	99.65	0.246	0.172	0.171	0.17	0.196	0.1931	RANDOM	23.921

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]
-0.57			0.13		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.453
r_dihedral_angle_4_deg	19.042
r_dihedral_angle_3_deg	12.019
r_dihedral_angle_1_deg	11.759
r_scangle_it	2.954
r_scbond_it	2.123
r_angle_refined_deg	1.519
r_mcangle_it	1.009
r_mcbond_it	0.987
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.205
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.107
r_metal_ion_refined	0.048
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2176
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	16

Software

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