3N25 | pdb_00003n25

The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop vapor diffusion	5.5	298	60 mM Succinate (pH 5.5), 5.8 mM sodium pyruvate, 2.4 mM MnCl2, 450 mM KCl, 444 mM Proline and a range of 18 to 20% PEG 8000., hanging drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.373	α = 95.18
b = 108.747	β = 93.38
c = 144.256	γ = 112.23

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	100	IMAGE PLATE	RIGAKU RAXIS IV++		2008-07-18		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R	1.54

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	2.4	50	83.6	0.123	8.9	3.5		146924

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	2.4	2.49	78.8		0.504		3	13799

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 (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	2.41	36.59	146918	7394	82.98	0.207	0.204	0.21	0.268	0.28	RANDOM	5.045

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]
0.56	0.24	0.3	-0.36	0.14	0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.381
r_dihedral_angle_4_deg	16.233
r_dihedral_angle_3_deg	15.039
r_dihedral_angle_1_deg	5.275
r_scangle_it	1.482
r_angle_refined_deg	1.125
r_scbond_it	0.893
r_mcangle_it	0.497
r_mcbond_it	0.269
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31683
Nucleic Acid Atoms
Solvent Atoms	1427
Heterogen Atoms	314

Software

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