3ZOU

Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696, and substrate geranyl pyrophosphate.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1815% GLYCEROL, 0.2 M MGCL2, 20% PEG6000, 0.1 M TRIS PH 8, 0.274 MM GPP, 10 MM SPB02696, 10% METHANOL, 1% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.0339.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.04α = 90
b = 98.64β = 90
c = 130.46γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-10-09MSINGLE 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
11.5530.6796.90.0613.14.2770891.913.2
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)
11.551.5875.80.541.92.8

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 3ZCD1.5530.6973178387496.830.163350.161690.19541RANDOM18.751
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]
0.89-0.42-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.302
r_dihedral_angle_4_deg17.51
r_dihedral_angle_3_deg13.51
r_dihedral_angle_1_deg5.199
r_angle_refined_deg1.894
r_angle_other_deg1.295
r_symmetry_vdw_refined0.304
r_nbd_refined0.273
r_symmetry_vdw_other0.234
r_nbd_other0.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.302
r_dihedral_angle_4_deg17.51
r_dihedral_angle_3_deg13.51
r_dihedral_angle_1_deg5.199
r_angle_refined_deg1.894
r_angle_other_deg1.295
r_symmetry_vdw_refined0.304
r_nbd_refined0.273
r_symmetry_vdw_other0.234
r_nbd_other0.211
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.185
r_xyhbond_nbd_other0.179
r_chiral_restr0.112
r_nbtor_other0.1
r_symmetry_hbond_refined0.074
r_metal_ion_refined0.063
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms4093
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing