5GUK

Crystal structure of apo form of cyclolavandulyl diphosphate synthase (CLDS) from Streptomyces sp. CL190


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100mM Tris HCl pH 7.0, 1M sodium citrate tribasic, 200mM NaCl
Crystal Properties
Matthews coefficientSolvent content
1.9236.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.025α = 90
b = 87.514β = 90
c = 113.548γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702014-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1Photon FactoryAR-NE3A

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
1269.321000.11721.8727009
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.030.521

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT269.3225558130799.430.194480.192350.23523RANDOM32.729
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]
-0.010.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.007
r_dihedral_angle_4_deg21.773
r_dihedral_angle_3_deg15.308
r_dihedral_angle_1_deg6.333
r_long_range_B_other6.07
r_long_range_B_refined6.068
r_scangle_other4.94
r_scbond_it3.268
r_scbond_other3.267
r_mcangle_it3.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.007
r_dihedral_angle_4_deg21.773
r_dihedral_angle_3_deg15.308
r_dihedral_angle_1_deg6.333
r_long_range_B_other6.07
r_long_range_B_refined6.068
r_scangle_other4.94
r_scbond_it3.268
r_scbond_other3.267
r_mcangle_it3.208
r_mcangle_other3.207
r_mcbond_it2.411
r_mcbond_other2.401
r_angle_refined_deg1.678
r_angle_other_deg0.991
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3406
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms2

Software

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