1HDI | pdb_00001hdi

Pig muscle 3-PHOSPHOGLYCERATE KINASE complexed with 3-PG and MgADP.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		THE STARTING MODEL WAS CHOSEN AS THE STRUCTURE OF THE MNADP BINARY COMPLEX OF PIG MUSCLE PGK CRYSTALLISED IN THE PRESENCE OF AMMONIUM SULPHATE (MAY ET AL., PERSONAL COMM.).

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	288	THE ENZYME WAS DIALYSED IN 30 MM NAK-PHOSPHATE BUFFER, PH=8.0. SINGLE CRYSTALS WERE GROWN AT 15C WITHIN A FEW WEEKS IN HANGING DROPS (10-15 ML EACH) INITIALLY CONTAINING 1.25 M NAK-PHOSPHATE (PH=8.0), 100 MM 3-PG, 25 MM MGCL2, 20 MM ADP, 10 MM DITHIOTHREITOL, 0.02% NAN3 AND 15 MG/ML PGK. RESERVOIR SOLUTIONS CONTAINED 2.4-2.75 M NAK-PHOSPHATE(PH=8.0)., pH 7.70

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.5	α = 90
b = 105.2	β = 98.4
c = 35.9	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	MARRESEARCH		1997-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX7.2		SRS	PX7.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	20	95.6	0.081	0.081	17	2.4		34292			21.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.88	98.1		0.244	0.244	3	2.3

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	THE STARTING MODEL WAS CHOSEN AS THE STRUCTURE OF THE MNADP BINARY COMPLEX OF PIG MUSCLE PGK CRYSTALLISED IN THE PRESENCE OF AMMONIUM SULPHATE (MAY ET AL., PERSONAL COMM.).	1.8	20	32755	1662	95.5	0.207	0.207	0.262	RANDOM	16.5

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
x_dihedral_angle_d	24.7
x_improper_angle_d	2.4
x_angle_deg	1.62
x_bond_d	0.011
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3037
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	35

Software

Software
Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.