3ZMC

Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound substrate molecule Geranyl pyrophosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZCDPDB ENTRY 3ZCD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.15 M MGCL2, 20% PEG8000, 0.1 M TRISCL PH 8
Crystal Properties
Matthews coefficientSolvent content
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.963α = 90
b = 98.778β = 90
c = 130.554γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.8740.8399.90.119.24.946143215.5
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)
11.871.911000.651.75

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 DIFFRACTIONSIRTHROUGHOUTPDB ENTRY 3ZCD1.8740.8643687227599.490.207110.204890.2505RANDOM20.409
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]
1.4-0.75-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.542
r_dihedral_angle_4_deg18.618
r_dihedral_angle_3_deg13.926
r_dihedral_angle_1_deg5.145
r_angle_refined_deg1.864
r_angle_other_deg1.286
r_nbd_refined0.274
r_symmetry_vdw_refined0.261
r_symmetry_vdw_other0.233
r_nbd_other0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.542
r_dihedral_angle_4_deg18.618
r_dihedral_angle_3_deg13.926
r_dihedral_angle_1_deg5.145
r_angle_refined_deg1.864
r_angle_other_deg1.286
r_nbd_refined0.274
r_symmetry_vdw_refined0.261
r_symmetry_vdw_other0.233
r_nbd_other0.215
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.146
r_chiral_restr0.111
r_nbtor_other0.099
r_metal_ion_refined0.095
r_xyhbond_nbd_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4068
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing