7KJD

F96M epi-isozizaene synthase: complex with 3 Mg2+ and risedronate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KB9PDB entry 3KB9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.08 mM Bis-Tris, pH 5.5, 0.02 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 26% PEG3350, 2% w/v benzamidine HCl
Crystal Properties
Matthews coefficientSolvent content
2.1342.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.82α = 90
b = 47.08β = 96.31
c = 75.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.978APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.552.599.10.9826.13.35862015.78
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.530.694

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 3KB91.552.51.3458547585395.120.21630.21520.245822.7
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
f_dihedral_angle_d5.7972
f_angle_d0.7675
f_chiral_restr0.042
f_bond_d0.0055
f_plane_restr0.0054
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2688
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms25

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing