1E89

ON THE MECHANISM OF CYANOGENESIS CATALYZED BY HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA. CRYSTAL STRUCTURE OF ACTIVE SITE MUTANT SER80ALA IN COMPLEX WITH ACETONE CYANOHYDRIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DWOPDB ENTRY 1DWO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.80.1 M NACITRAT, PH 4.8, 6% PEG8000, 28% MPD
Crystal Properties
Matthews coefficientSolvent content
4.571

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.18α = 90
b = 106.18β = 90
c = 188.15γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.12096.70.0658.84.36333616.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.298.40.1413.44.2

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DWO2.18260467602497.30.180.180.219RANDOM22.5
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
x_dihedral_angle_d24
x_scangle_it5.42
x_scbond_it3.53
x_angle_deg2.8
x_mcangle_it2.33
x_mcbond_it1.58
x_improper_angle_d1.13
x_bond_d0.015
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24
x_scangle_it5.42
x_scbond_it3.53
x_angle_deg2.8
x_mcangle_it2.33
x_mcbond_it1.58
x_improper_angle_d1.13
x_bond_d0.015
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4176
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms

Software

Software
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing