2PY7 | pdb_00002py7

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	A 2ul drop with 4 mg/ml protein, 20 mM Tris-HCl (pH 7.6), 0.5 mM EDTA, 5 mM ADP, 2.5 mM phosphoenolpyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 0.1 M sodium acetate, 0.05 M sodium cacodylate (pH 6.5), 15% PEG 8000 was allowed to equilibrate with a 1 ml well of 0.2 M sodium aceate, 0.1 M sodium cacodylate 30% PEG 8000. After a week a 0.1 x 0.1 x 0.4 mm crystal was removed and put in a small volume of well solution with 30% glycerol added. The crystal was put into a loop and flash cooled in liquid notrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.999	α = 90
b = 95.663	β = 96.12
c = 46.319	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	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.919	APS	14-BM-C

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	2.02	99	85.95	0.1		2.95	89783	36560		13.96

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.28	59.6		0.14	4.9	1.17

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1AYL	2.2	18.48	24587	1282	94.1	0.15795	0.15484	0.16	0.21792	0.15	RANDOM	14.325

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		-0.03	0.04		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.833
r_dihedral_angle_4_deg	16.456
r_dihedral_angle_3_deg	13.948
r_dihedral_angle_1_deg	5.684
r_scangle_it	2.205
r_scbond_it	1.372
r_angle_refined_deg	1.234
r_mcangle_it	0.869
r_mcbond_it	0.523
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.3
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.107
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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_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	4133
Nucleic Acid Atoms
Solvent Atoms	570
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing