1XBY

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase E112D/T169A mutant with bound D-ribulose 5-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527316% PEG 5000 methyl ether, 100 mM BTP pH 7.0, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.785α = 90
b = 41.906β = 97.46
c = 91.225γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2004-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.961APS19-ID

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
11.589298.40.05827.741056863096
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)
1.581.6489.80.3353.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5891.295869258962314298.270.159670.159670.157920.19279RANDOM18.72
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]
-1.32-0.142.95-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.123
r_scangle_it5.531
r_scbond_it3.776
r_mcangle_it2.568
r_angle_refined_deg1.661
r_mcbond_it1.642
r_angle_other_deg0.865
r_symmetry_vdw_other0.296
r_nbd_refined0.27
r_nbd_other0.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.123
r_scangle_it5.531
r_scbond_it3.776
r_mcangle_it2.568
r_angle_refined_deg1.661
r_mcbond_it1.642
r_angle_other_deg0.865
r_symmetry_vdw_other0.296
r_nbd_refined0.27
r_nbd_other0.251
r_symmetry_hbond_refined0.218
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_refined0.166
r_chiral_restr0.103
r_nbtor_other0.082
r_bond_refined_d0.018
r_metal_ion_refined0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3264
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms28

Software

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