2PXZ

E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon dioxide and oxaloacetate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	294	8ul drop with 8ug/ml protein, 2mM ADP, 5mM MgCl2, 10 uM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate and 12% w/v PEG 4000 was allowed to equilibrate with a 1 ml reservoir of 100 mM sodium aceate, 200 mM ammonium acetate and 27% PEG 4000. After crystals grew for one week 2ul of a 1 mM EDTA and saturated sodium oxaloacetate solution was added to the drop. 5 ul of glycerol was added to the drop. A 0.1 x 0.1 x 0.3 mm crystal was removed with a loop and flash cooled in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.556	α = 90
b = 94.302	β = 95.54
c = 46.354	γ = 90

Symmetry
Space Group	C 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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.3317	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.83	47.14	100	0.085		3.6	595228	171743		13.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.23	2.28	100		2.5	3.5	24303

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.23	38.32	24889	1322	100	0.17585	0.17277	0.23421	RANDOM	20.323

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]
0.02		0.01	-0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.049
r_dihedral_angle_4_deg	16.591
r_dihedral_angle_3_deg	15.914
r_dihedral_angle_1_deg	7.025
r_scangle_it	4.049
r_scbond_it	2.767
r_angle_refined_deg	1.932
r_mcangle_it	1.653
r_mcbond_it	1.047
r_symmetry_hbond_refined	0.374
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.143
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4007
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing