3E0V | pdb_00003e0v

Crystal structure of pyruvate kinase from Leishmania mexicana in complex with sulphate ions

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, chain G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	277	20% Saturated ammonium sulphate, 100mM Na citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.51	72.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 261.955	α = 90
b = 261.955	β = 90
c = 185.541	γ = 90

Symmetry
Space Group	P 42 21 2

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 4	Mirrors	2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

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	3.3	99.06	89.4	0.075	0.075	8.9	3.1		86237

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	3.3	3.48	89.4		0.496	1.6	2.7

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, chain G	3.3	99.06	80266	4286	87.18	0.22987	0.22663	0.22	0.28958	0.28	RANDOM	74.381

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]
0.98			0.98		-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.357
r_dihedral_angle_3_deg	20.562
r_dihedral_angle_4_deg	18.177
r_dihedral_angle_1_deg	6.152
r_scangle_it	2.297
r_scbond_it	1.373
r_angle_refined_deg	1.244
r_mcangle_it	1.001
r_mcbond_it	0.523
r_nbtor_refined	0.309
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.192
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.084
r_bond_refined_d	0.009
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_refined
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	22676
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	218

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing