6LOO | pdb_00006loo

Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YO8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.3298PEG3350, Ammonium Acetate, Magnesium Chloride, Methanol
Crystal Properties
Matthews coefficientSolvent content
2.1643.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.87α = 94.63
b = 53.48β = 104.72
c = 76.54γ = 113.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2018-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9948.1297.80.0950.110.99813.653.9054714134.108
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0496.60.8420.9780.53223.93

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5yo81.9948.1244802233997.880.18130.1790.180.22460.23RANDOM32.585
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]
1.490.76-0.11-0.930.28-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.355
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg14.514
r_dihedral_angle_1_deg5.663
r_angle_refined_deg1.32
r_angle_other_deg1.281
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.355
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg14.514
r_dihedral_angle_1_deg5.663
r_angle_refined_deg1.32
r_angle_other_deg1.281
r_chiral_restr0.072
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 Atoms5767
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms116

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing