3H6O | pdb_00003h6o

Activator-Bound Structure of Human Pyruvate Kinase M2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GQY	Direct placement of PDB entry 3GQY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	25% PEG3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 0.005M activator, pH 5.5, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.343	α = 90
b = 155.69	β = 108.04
c = 101.789	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		IMAGE PLATE	RIGAKU RAXIS		2009-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	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	2	20	97	0.077	11.2	3.6		157058

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	2.07	96.8		0.947		3.6	15625

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		THROUGHOUT	Direct placement of PDB entry 3GQY	2	19.96	152479	1859	94.23	0.248	0.247	0.28	0.287	0.31	thin shells (SFTOOLS)	33.749

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]
-1.396		-2.3	1.67		-1.698

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_2_deg	32.837
f_dihedral_angle_4_deg	16.519
f_dihedral_angle_3_deg	13.054
f_dihedral_angle_1_deg	5.402
f_mcangle_it	1.542
f_scangle_it	1.457
f_angle_refined_deg	1.162
f_mcbond_it	1.073
f_scbond_it	1.025
f_angle_other_deg	0.862
f_mcbond_other	0.273
f_symmetry_vdw_other	0.265
f_nbd_refined	0.189
f_nbd_other	0.186
f_symmetry_hbond_refined	0.184
f_nbtor_refined	0.164
f_xyhbond_nbd_refined	0.129
f_nbtor_other	0.081
f_chiral_restr	0.062
f_symmetry_vdw_refined	0.021
f_bond_refined_d	0.012
f_gen_planes_refined	0.003
f_bond_other_d	0.002
f_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14722
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	157

Software

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