3UCA

Crystal structure of isoprenoid synthase (target EFI-501974) from clostridium perfringens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KRFPDB ENTRY 3KRF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1M BIS-TRIS, 0.2M SODIUM CHLORIDE, PH 5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294
Crystal Properties
Matthews coefficientSolvent content
2.2344.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.117α = 90
b = 70.117β = 90
c = 228.136γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2011-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
125099.80.1325.77.245199-536.585
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.031001.16.2

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 3KRF236.4843574140299.830.190590.189250.22996RANDOM47.279
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]
-0.38-0.19-0.380.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.34
r_dihedral_angle_3_deg16.217
r_dihedral_angle_4_deg12.332
r_scangle_it11.339
r_scbond_it7.746
r_mcangle_it5.325
r_dihedral_angle_1_deg4.468
r_mcbond_it3.584
r_angle_refined_deg1.109
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.34
r_dihedral_angle_3_deg16.217
r_dihedral_angle_4_deg12.332
r_scangle_it11.339
r_scbond_it7.746
r_mcangle_it5.325
r_dihedral_angle_1_deg4.468
r_mcbond_it3.584
r_angle_refined_deg1.109
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4240
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms

Software

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