3ZMB

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
180.2 M MGCL2, 20% PEG6000, 0.1 M TRIS PH 8
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.56α = 90
b = 98.84β = 90
c = 131.5γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-04-10MSINGLE 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
11.932.8899.30.127.13.743864216.9
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)
11.9299.50.661.93.9

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 3ZCD1.932.941464219698.740.191140.188490.24095RANDOM22.275
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]
0.69-1.110.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.993
r_dihedral_angle_4_deg20.386
r_dihedral_angle_3_deg14.276
r_dihedral_angle_1_deg5.472
r_angle_refined_deg1.662
r_angle_other_deg1.177
r_symmetry_vdw_refined0.325
r_nbd_refined0.278
r_symmetry_vdw_other0.278
r_xyhbond_nbd_other0.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.993
r_dihedral_angle_4_deg20.386
r_dihedral_angle_3_deg14.276
r_dihedral_angle_1_deg5.472
r_angle_refined_deg1.662
r_angle_other_deg1.177
r_symmetry_vdw_refined0.325
r_nbd_refined0.278
r_symmetry_vdw_other0.278
r_xyhbond_nbd_other0.242
r_symmetry_hbond_refined0.232
r_nbd_other0.219
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.182
r_nbtor_other0.101
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4104
Nucleic Acid Atoms
Solvent Atoms609
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing