5UD4

Class II fructose-1,6-bisphosphate aldolase H180Q variant of Helicobacter pylori with TBP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C4U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8297PEG 8000, PEG 1000, Calcium acetate, Tris-Acetic acid buffer
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.391α = 81.98
b = 62.59β = 75.74
c = 64.817γ = 74.23
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.545.13586.230.076380.9857.071.883963

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3C4U1.545.1350.1279526383486.230.13590.13380.1769
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.222
f_angle_d0.933
f_chiral_restr0.075
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4534
Nucleic Acid Atoms
Solvent Atoms786
Heterogen Atoms46

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing