2OLR

Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase complexed with carbon dioxide, Mg2+, ATP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AYL	pdb entry 1AYL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	293	8 microL drops: 8 mg/ml protein concentration, 2 mM ATP, 5 mM oxalate, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate, 12% PEG 4000, 1 ml resevoir: 100 mM sodium acetate, 200 mM ammonuim acetate, 27% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.854	α = 90
b = 95.564	β = 96.3
c = 46.476	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	105	CCD	ADSC QUANTUM 315	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

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	1.4	75.8	99.3	0.078	9.4	3.5	105079	105079		5

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)
	1.4	1.45	97.8		0.402	2.1	3.35	15056

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1AYL	1.6	75.81	67499	3557	99.59	0.17573	0.17451	0.19842	RANDOM	14.86

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]
-0.88		-0.16	0.93		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.374
r_dihedral_angle_4_deg	14.817
r_dihedral_angle_3_deg	12.188
r_dihedral_angle_1_deg	5.735
r_scangle_it	2.958
r_scbond_it	1.879
r_angle_refined_deg	1.292
r_mcangle_it	1.142
r_mcbond_it	0.722
r_nbtor_refined	0.308
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.167
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
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	4120
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing