8IW2

Entamoeba histolytica Pyruvate kinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	289	50mM MES buffer, pH 6.2, 0.2M LiCl2, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.801	α = 90
b = 89.536	β = 90
c = 37.138	γ = 90

Symmetry
Space Group	P 21 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	80	PIXEL	DECTRIS PILATUS 6M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.977	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.75	42.937	99	0.115	0.109	0.047	0.998	15.5	9.3		29332

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	99.1		0.956	0.485	0.718	2	9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.75	42.937	29295	1526	98.7	0.172	0.1706	0.2017	22.543

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]
-1.628			-1.505		3.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.425
r_dihedral_angle_3_deg	13.606
r_dihedral_angle_2_deg	10.242
r_lrange_it	7.242
r_lrange_other	7.227
r_dihedral_angle_1_deg	6.814
r_scangle_it	6.376
r_scangle_other	6.374
r_scbond_other	4.359
r_scbond_it	4.358
r_mcangle_other	3.145
r_mcangle_it	3.143
r_mcbond_it	2.4
r_mcbond_other	2.396
r_angle_refined_deg	1.899
r_angle_other_deg	0.617
r_xyhbond_nbd_refined	0.264
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.2
r_nbd_other	0.188
r_nbtor_refined	0.179
r_xyhbond_nbd_other	0.13
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2551
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHELXCD	phasing