1Q6O

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-gulonaet 6-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH729816% MePEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, microbatch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1341.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.24α = 90
b = 41.775β = 97.15
c = 90.958γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C1.0247APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.20210092.429.61315682
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.2021.2469.74.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.20291.29131568124961660792.020.14180.14080.1605RANDOM14.279
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]
-0.670.221.01-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.906
r_scangle_it4.279
r_sphericity_free3.791
r_sphericity_bonded3.617
r_scbond_it2.931
r_mcangle_it2.452
r_angle_other_deg2.07
r_mcbond_it1.646
r_angle_refined_deg1.511
r_rigid_bond_restr1.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.906
r_scangle_it4.279
r_sphericity_free3.791
r_sphericity_bonded3.617
r_scbond_it2.931
r_mcangle_it2.452
r_angle_other_deg2.07
r_mcbond_it1.646
r_angle_refined_deg1.511
r_rigid_bond_restr1.401
r_symmetry_vdw_other0.293
r_nbd_other0.25
r_nbd_refined0.233
r_xyhbond_nbd_refined0.187
r_symmetry_vdw_refined0.165
r_symmetry_hbond_refined0.164
r_chiral_restr0.12
r_nbtor_other0.089
r_bond_refined_d0.012
r_gen_planes_other0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3297
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing