3ZCD

Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LJIPDB ENTRY 3LJI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525% PEG3350, 0.2 M NAF, 0.1 M BISTRISPROPANE PH 6.5
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.18α = 90
b = 98.63β = 90
c = 131.07γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.5565.5499.50.17.23.778917214.6
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)
11.551.6399.40.363.43.4

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 3LJI1.5525.8474536395499.170.153620.150990.20378RANDOM22.379
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]
-1.513.78-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.658
r_dihedral_angle_2_deg32.922
r_dihedral_angle_4_deg21.172
r_sphericity_bonded17.454
r_dihedral_angle_3_deg13.41
r_rigid_bond_restr6.72
r_dihedral_angle_1_deg4.9
r_angle_refined_deg1.608
r_angle_other_deg1.176
r_symmetry_vdw_refined0.268
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.658
r_dihedral_angle_2_deg32.922
r_dihedral_angle_4_deg21.172
r_sphericity_bonded17.454
r_dihedral_angle_3_deg13.41
r_rigid_bond_restr6.72
r_dihedral_angle_1_deg4.9
r_angle_refined_deg1.608
r_angle_other_deg1.176
r_symmetry_vdw_refined0.268
r_nbd_refined0.263
r_nbd_other0.215
r_symmetry_vdw_other0.198
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.156
r_nbtor_other0.103
r_chiral_restr0.094
r_symmetry_hbond_refined0.059
r_xyhbond_nbd_other0.052
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.005
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4095
Nucleic Acid Atoms
Solvent Atoms559
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing