7BR1

Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6JHC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298potassium thiocyanate, sodium acetate pH 5.5, 10% w/v PEG 8000, 10% w/v PEG 1000, benzaldehyde
Crystal Properties
Matthews coefficientSolvent content
2.1242.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.934α = 90
b = 32.763β = 102.84
c = 84.632γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.2582.5171000.0530.0580.02218.16.68489184891
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)
11.251.321000.8390.8390.9160.3620.96.3

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 REPLACEMENTTHROUGHOUT6JHC1.2541.9880582429699.950.14070.14030.1475RANDOM13.322
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.359
r_dihedral_angle_4_deg13.973
r_dihedral_angle_3_deg10.775
r_dihedral_angle_1_deg7.088
r_angle_other_deg1.392
r_angle_refined_deg1.357
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.359
r_dihedral_angle_4_deg13.973
r_dihedral_angle_3_deg10.775
r_dihedral_angle_1_deg7.088
r_angle_other_deg1.392
r_angle_refined_deg1.357
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2544
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms52

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction