4I7E

Crystal Structure of the Bacillus stearothermophilus Phosphofructokinase Mutant D12A in Complex with PEP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62890.1 M sodium citrate tribasic dehydrate pH 5.6, 20% v/v 2-propanol, 20% w/v polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6253.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.65α = 90
b = 112.96β = 90
c = 131.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MIRRORS2009-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
1265.52970.05313.33.619446129
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)
122.0778.20.3892.72.88

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3U39256.794460944604715970.1910.1890.235RANDOM47.67
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]
-0.110.39-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.316
r_dihedral_angle_3_deg15.254
r_dihedral_angle_4_deg14.146
r_dihedral_angle_1_deg8.92
r_scangle_it2.497
r_scbond_it1.621
r_angle_refined_deg1.355
r_mcangle_it1.165
r_angle_other_deg0.914
r_mcbond_it0.685
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.316
r_dihedral_angle_3_deg15.254
r_dihedral_angle_4_deg14.146
r_dihedral_angle_1_deg8.92
r_scangle_it2.497
r_scbond_it1.621
r_angle_refined_deg1.355
r_mcangle_it1.165
r_angle_other_deg0.914
r_mcbond_it0.685
r_symmetry_vdw_other0.257
r_nbd_refined0.206
r_nbd_other0.202
r_nbtor_refined0.17
r_symmetry_hbond_refined0.168
r_symmetry_vdw_refined0.157
r_xyhbond_nbd_refined0.155
r_mcbond_other0.133
r_nbtor_other0.086
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9482
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms40

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction