4LLT

Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP 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, 20% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.899α = 90
b = 83.117β = 108.95
c = 71.332γ = 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-ID0.9793APS31-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
11.555096.10.07516.23.88134178181
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)
11.551.5893.70.6842.13.7

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 3LVS1.5526.4674260389696.050.175640.174180.20379RANDOM20.307
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]
-0.230.31-0.220.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.573
r_dihedral_angle_4_deg18.102
r_dihedral_angle_3_deg13.777
r_long_range_B_refined5.871
r_long_range_B_other5.844
r_dihedral_angle_1_deg5.233
r_scangle_other5.229
r_scbond_it3.676
r_scbond_other3.675
r_mcangle_it2.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.573
r_dihedral_angle_4_deg18.102
r_dihedral_angle_3_deg13.777
r_long_range_B_refined5.871
r_long_range_B_other5.844
r_dihedral_angle_1_deg5.233
r_scangle_other5.229
r_scbond_it3.676
r_scbond_other3.675
r_mcangle_it2.842
r_mcangle_other2.841
r_mcbond_it2.072
r_mcbond_other2.071
r_angle_refined_deg1.516
r_angle_other_deg0.976
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_gen_planes_other0.005
r_bond_other_d0.003
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 Atoms4335
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms62

Software

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