1WBH

Crystal structure of the E45N mutant from KDPG aldolase from Escherichia coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EUAPDB ENTRY 1EUA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.075M SODIUM ACETATE, 0.1M AMMONIUM SULPHATE, 27%W/V PEG4000, pH 4.60
Crystal Properties
Matthews coefficientSolvent content
2.346.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.492α = 90
b = 84.244β = 90
c = 132.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2002-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.554099.40.083.4891811.5
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)
11.551.6998.80.363.2

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 1EUA1.5540.16829744409980.170.1680.217RANDOM20.93
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]
0.030.08-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.456
r_dihedral_angle_4_deg16.032
r_dihedral_angle_3_deg14.133
r_scangle_it5.493
r_dihedral_angle_1_deg5.359
r_scbond_it4.087
r_mcangle_it2.32
r_mcbond_it1.664
r_angle_refined_deg1.657
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.456
r_dihedral_angle_4_deg16.032
r_dihedral_angle_3_deg14.133
r_scangle_it5.493
r_dihedral_angle_1_deg5.359
r_scbond_it4.087
r_mcangle_it2.32
r_mcbond_it1.664
r_angle_refined_deg1.657
r_nbtor_refined0.315
r_symmetry_vdw_refined0.249
r_nbd_refined0.237
r_symmetry_hbond_refined0.209
r_xyhbond_nbd_refined0.17
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4700
Nucleic Acid Atoms
Solvent Atoms720
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing