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Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696, and substrate geranyl pyrophosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZCD PDB ENTRY 3ZCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 15% 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 coefficient Solvent content 2.03 39.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.04 α = 90 b = 98.64 β = 90 c = 130.46 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2012-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 30.67 96.9 0.06 13.1 4.2 77089 1.9 13.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 75.8 0.54 1.9 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIR THROUGHOUT PDB ENTRY 3ZCD 1.55 30.69 73178 3874 96.83 0.16335 0.16169 0.1749 0.19541 0.2043 RANDOM 18.751
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.302 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 13.51 r_dihedral_angle_1_deg 5.199 r_angle_refined_deg 1.894 r_angle_other_deg 1.295 r_symmetry_vdw_refined 0.304 r_nbd_refined 0.273 r_symmetry_vdw_other 0.234 r_nbd_other 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.302 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 13.51 r_dihedral_angle_1_deg 5.199 r_angle_refined_deg 1.894 r_angle_other_deg 1.295 r_symmetry_vdw_refined 0.304 r_nbd_refined 0.273 r_symmetry_vdw_other 0.234 r_nbd_other 0.211 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.185 r_xyhbond_nbd_other 0.179 r_chiral_restr 0.112 r_nbtor_other 0.1 r_symmetry_hbond_refined 0.074 r_metal_ion_refined 0.063 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 Atoms Number Protein Atoms 4093 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling REFMAC phasing