Experiment: 1KC7

Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	303	54% saturated ammonium sulfate, 100mM Hepes buffer (pH 7.0), 9mg/ml protein solution consisting of: 20mM imidazole buffer (pH 6.5), 100mM KCl, 40mM phosphonopyruvate, 5mM MgCl2, 0.1mM EDTA, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.21	α = 90
b = 58.42	β = 94.99
c = 102.55	γ = 90

Symmetry
Space Group	P 1 2 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	CCD	MARRESEARCH	mirror	2001-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	1.73	25	95.1	0.114	26.6	3.4	104444	104444			40.8

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	1.73	1.79	81.4		0.52	4.1	3.1	14814

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1DIK	2.2	25	2	52306	51903	2584	96.3	0.198	0.2408	0.269	0.2832	RANDOM

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
c_angle_deg	1.9
c_bond_d	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6752
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

Software
Software Name	Purpose
CNS	refinement
X-GEN	data reduction
X-GEN	data scaling