1ZXX

The crystal structure of phosphofructokinase from Lactobacillus delbrueckii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M Tris pH 7.5, 1 mM DTT, 1 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.014α = 90
b = 135.014β = 90
c = 77.66γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.0APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.852098.50.0570.05750.61833708

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.852033708178098.550.223650.222150.25132RANDOM41.108
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]
-0.82-0.41-0.821.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.385
r_dihedral_angle_3_deg15.849
r_dihedral_angle_4_deg14.623
r_dihedral_angle_1_deg5.102
r_scangle_it2.3
r_scbond_it1.493
r_mcangle_it1.072
r_angle_refined_deg1.07
r_mcbond_it0.621
r_symmetry_vdw_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.385
r_dihedral_angle_3_deg15.849
r_dihedral_angle_4_deg14.623
r_dihedral_angle_1_deg5.102
r_scangle_it2.3
r_scbond_it1.493
r_mcangle_it1.072
r_angle_refined_deg1.07
r_mcbond_it0.621
r_symmetry_vdw_refined0.221
r_nbd_refined0.19
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.109
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms2387
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing