3QV6

Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue 80.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	277	7-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.03	69.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.053	α = 90
b = 127.495	β = 116.19
c = 118.168	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1	Diamond	I03

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	2.85	86.08	100	0.083	0.094	11.8	4.6	181103	39558	2.85	2.85	77.4

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	2.85	2.93	100		0.541	0.612	2.5	4.5	2880

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1PKL	2.85	86.08	37465	1979	100	0.23699	0.23541	0.26709	RANDOM	72.567

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]
0.4		-0.32	0.04		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.739
r_dihedral_angle_3_deg	15.196
r_dihedral_angle_4_deg	11.965
r_dihedral_angle_1_deg	4.4
r_scangle_it	0.91
r_angle_refined_deg	0.873
r_scbond_it	0.478
r_mcangle_it	0.473
r_mcbond_it	0.254
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6745
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement