4LLS

Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with IPP, GSPP, and calcium bound in active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LVSPDB ENTRY 3LVS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.2 M calcium acetate, 0.1 M MES/NaOH, pH 6.0, 20% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.095α = 90
b = 83.032β = 108.87
c = 71.386γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2013-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.55099.70.07415.23.89001289715
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)
11.51.5399.90.6322.13.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3LVS1.526.585196449599.560.170150.168770.19544RANDOM21.757
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]
0.070.130.4-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.063
r_dihedral_angle_4_deg21.052
r_dihedral_angle_3_deg13.942
r_long_range_B_refined6.411
r_long_range_B_other6.411
r_scangle_other5.706
r_dihedral_angle_1_deg5.3
r_scbond_it3.974
r_scbond_other3.974
r_mcangle_it2.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.063
r_dihedral_angle_4_deg21.052
r_dihedral_angle_3_deg13.942
r_long_range_B_refined6.411
r_long_range_B_other6.411
r_scangle_other5.706
r_dihedral_angle_1_deg5.3
r_scbond_it3.974
r_scbond_other3.974
r_mcangle_it2.911
r_mcangle_other2.911
r_mcbond_it2.139
r_mcbond_other2.134
r_angle_refined_deg1.385
r_angle_other_deg0.842
r_chiral_restr0.086
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.006
r_bond_other_d0.002
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 Atoms4332
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms72

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling