3ME3

Activator-Bound Structure of Human Pyruvate Kinase M2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	291	25% w/v PEG-3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, 0.005M activator (from 0.1M stock solution in DMSO)., pH 6.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.882	α = 90
b = 152.564	β = 103.17
c = 93.036	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU SATURN A200		2010-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.95	40	99.8	0.08	10.7	3.6		158866

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	1.95	1.98	97.4		0.857		3	7719

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		THROUGHOUT	isomorphous pdb entry 3GQY	1.95	26.714	158798	1914	99.682	0.219	0.219	0.262	thin shells (sftools)	23.419

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]
-0.709		-1.136	0.028		0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.075
r_dihedral_angle_4_deg	15.671
r_dihedral_angle_3_deg	13.272
r_dihedral_angle_1_deg	5.71
r_scangle_it	3.245
r_scbond_it	2.045
r_angle_refined_deg	1.425
r_mcangle_it	1.284
r_angle_other_deg	0.906
r_mcbond_it	0.723
r_mcbond_other	0.18
r_chiral_restr	0.078
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15143
Nucleic Acid Atoms
Solvent Atoms	675
Heterogen Atoms	202

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling