8GY0 | pdb_00008gy0

Agrocybe pediades linalool sunthase (Ap.LS)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PS11ps1, 2wbu
experimental modelPDB 2WBU1ps1, 2wbu

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6295.1510mM MgCl2, 0.2 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5 and 18% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6253.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.925α = 90
b = 80.665β = 96.05
c = 69.906γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

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
11.985090.50.08929.75.848065
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)
11.982.010.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMADFREE R-VALUE1ps1, 2wbu1.98846.80444039183182.6810.2170.21440.220.27450.2866.281
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]
3.1790.546-6.0362.682
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.4
r_dihedral_angle_3_deg19.269
r_dihedral_angle_4_deg17.85
r_lrange_other11.69
r_lrange_it11.68
r_scangle_it8.904
r_scangle_other8.903
r_mcangle_other8.682
r_mcangle_it8.681
r_mcbond_it6.171
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5049
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MADSYSphasing