1GXS

Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with Inhibitor Benzoic Acid: a novel cyanogenic enzyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SC2PDB ENTRY 3SC2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.4100MM NA-CITRATE PH 5.4 USING 1.6 M AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
3.1661

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.7α = 90
b = 103.7β = 101.3
c = 90.6γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR571

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
12.31788.78.52100992215.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3882.95.72

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 3SC22.38250480512285.20.1650.1650.222RANDOM18.9
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_d25.1
x_scangle_it6.32
x_scbond_it4.42
x_mcangle_it3.91
x_angle_deg3.1
x_mcbond_it2.61
x_improper_angle_d1.21
x_bond_d0.017
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.1
x_scangle_it6.32
x_scbond_it4.42
x_mcangle_it3.91
x_angle_deg3.1
x_mcbond_it2.61
x_improper_angle_d1.21
x_bond_d0.017
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 Atoms6748
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms146

Software

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