3HQP | pdb_00003hqp

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	277	10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.486	α = 89.73
b = 151.14	β = 80.17
c = 160.319	γ = 71.64

Symmetry
Space Group	P 1

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	MAR CCD 165 mm	mirrors	2008-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.98	ESRF	ID23-1

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	2.3	41.96	94.7	0.095	8.2	1.9	913876	470114	2.3	2.3	41.2

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	2.3	2.42	90.8		0.638	1.3	1.3	65953

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 (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 1PKL	2.3	34.46	446260	23579	94.63	0.20111	0.19841	0.2	0.25198	0.25	RANDOM	42.789

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]
-2.77	0.29	0.16	-0.41	-0.84	2.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.789
r_dihedral_angle_4_deg	16.527
r_dihedral_angle_3_deg	16.234
r_dihedral_angle_1_deg	4.96
r_scangle_it	1.391
r_angle_refined_deg	1.106
r_scbond_it	0.87
r_mcangle_it	0.492
r_nbtor_refined	0.294
r_mcbond_it	0.254
r_metal_ion_refined	0.21
r_symmetry_vdw_refined	0.188
r_nbd_refined	0.182
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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	60784
Nucleic Acid Atoms
Solvent Atoms	4100
Heterogen Atoms	973

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
SCALA	data scaling