3GQY | pdb_00003gqy

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	1ZJH	pdb entry 1ZJH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	20% PEG3350, 0.2M diammonium tartrate, 0.005M activator, 0.005M ATP, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.149	α = 90
b = 152.952	β = 103.28
c = 93.159	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	IMAGE PLATE	RIGAKU RAXIS		2009-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	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	1.85	30	96.9	0.067	12.3	3.8		182520

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)
	1.85	1.92	94.3		0.969		3.8	17673

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 1ZJH	1.85	25	181606	2125	96.741	0.213	0.213	0.2135	0.238	0.2358	Thin shells (sftools)	25.794

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]
-0.63		-0.653	-0.083		0.413

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_2_deg	32.911
f_dihedral_angle_4_deg	13.57
f_dihedral_angle_3_deg	11.544
f_dihedral_angle_1_deg	4.994
f_scangle_it	1.732
f_mcangle_it	1.583
f_scbond_it	1.101
f_angle_refined_deg	1.014
f_mcbond_it	0.977
f_angle_other_deg	0.804
f_mcbond_other	0.22
f_chiral_restr	0.058
f_bond_refined_d	0.011
f_gen_planes_refined	0.003
f_bond_other_d	0.001
f_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15056
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	195

Software

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