2G50 | pdb_00002g50

The location of the allosteric amino acid binding site of muscle pyruvate kinase.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	60 mM Succinate (pH 5.5), 5.8 mM sodium pyruvate, 2.4 mM MnCl2, 450 mM KCl, and a range of 18 to 20% PEG 8000, 150 mM Alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.626	α = 95.15
b = 109.014	β = 93.45
c = 144.463	γ = 112.26

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 210	Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing	2005-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9795	NSLS	X6A

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	1.65	100	92.5	0.074	14.8	3.8	508417	508417

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	1.65	1.71	55.2	60.3	0.314	4.3	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	IF3W	1.65	76.47	508412	508412	25590	92.13	0.149	0.149	0.148	0.1459	0.174	0.1718	RANDOM	15.493

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.18
r_dihedral_angle_4_deg	16.837
r_dihedral_angle_3_deg	12.631
r_dihedral_angle_1_deg	5
r_scangle_it	3.005
r_scbond_it	1.799
r_angle_refined_deg	1.151
r_mcangle_it	0.918
r_mcbond_it	0.491
r_nbtor_refined	0.302
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.113
r_metal_ion_refined	0.085
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31708
Nucleic Acid Atoms
Solvent Atoms	4794
Heterogen Atoms	422

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing