7VB6

Crystal structure of hydroxynitrile lyase from Linum usitatissium complexed with (R)-2-hydroxy-2-methylbutanenitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VB3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.1 M BIS-TRIS, pH 6.5, 20% w/v polyethylene glycol monomethyl ether 5000
Crystal Properties
Matthews coefficientSolvent content
2.1642.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.178α = 90
b = 52.103β = 94.8
c = 169.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2020-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.723169.255970.1130.1230.0499.96.2168508168508
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.7231.8284.70.6630.6630.7230.2841.16.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7VB31.7449.85159549865398.590.16540.16330.2056RANDOM22.148
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]
-1.760.150.381.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.387
r_dihedral_angle_3_deg13.169
r_dihedral_angle_4_deg11.161
r_dihedral_angle_1_deg7.229
r_angle_refined_deg1.635
r_angle_other_deg1.37
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.387
r_dihedral_angle_3_deg13.169
r_dihedral_angle_4_deg11.161
r_dihedral_angle_1_deg7.229
r_angle_refined_deg1.635
r_angle_other_deg1.37
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12454
Nucleic Acid Atoms
Solvent Atoms1422
Heterogen Atoms328

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
MOSFLMdata reduction