1XBV

Crystal structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound D-ribulose 5-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529816% PEG 5000 methyl ether, 100 mM BTP, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.814α = 90
b = 41.471β = 96.65
c = 91.184γ = 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
11.669299.10.04215.83828173828172
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)
1.661.7298.20.43773.3

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 REPLACEMENTTHROUGHOUT1.6691.295164151641276299.070.163920.163920.162260.1939RANDOM20.559
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]
-0.470.831.39-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.302
r_scangle_it5.496
r_scbond_it3.773
r_mcangle_it2.725
r_mcbond_it1.719
r_angle_refined_deg1.648
r_angle_other_deg1.152
r_symmetry_vdw_other0.301
r_nbd_other0.251
r_nbd_refined0.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.302
r_scangle_it5.496
r_scbond_it3.773
r_mcangle_it2.725
r_mcbond_it1.719
r_angle_refined_deg1.648
r_angle_other_deg1.152
r_symmetry_vdw_other0.301
r_nbd_other0.251
r_nbd_refined0.236
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.186
r_chiral_restr0.107
r_metal_ion_refined0.105
r_symmetry_vdw_refined0.101
r_nbtor_other0.084
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms3286
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms28

Software

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