2OLR

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AYLpdb entry 1AYL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.42938 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 coefficientSolvent content
2.3146.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.854α = 90
b = 95.564β = 96.3
c = 46.476γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105CCDADSC QUANTUM 315mirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.475.899.30.0789.43.51050791050795
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4597.80.4022.13.3515056

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1AYL1.675.8167499355799.590.175730.174510.19842RANDOM14.86
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]
-0.88-0.160.93-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.374
r_dihedral_angle_4_deg14.817
r_dihedral_angle_3_deg12.188
r_dihedral_angle_1_deg5.735
r_scangle_it2.958
r_scbond_it1.879
r_angle_refined_deg1.292
r_mcangle_it1.142
r_mcbond_it0.722
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.374
r_dihedral_angle_4_deg14.817
r_dihedral_angle_3_deg12.188
r_dihedral_angle_1_deg5.735
r_scangle_it2.958
r_scbond_it1.879
r_angle_refined_deg1.292
r_mcangle_it1.142
r_mcbond_it0.722
r_nbtor_refined0.308
r_nbd_refined0.193
r_symmetry_hbond_refined0.167
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.118
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms4120
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
PHASERphasing