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Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.
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 0.2 M MGCL2, 20% PEG6000, 0.1 M TRISCL PH 8
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.16 α = 90 b = 98.84 β = 90 c = 131.55 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 2011-04-10 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 1.85 32.26 99.6 0.12 8.2 4.5 47364 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 1.85 1.95 100 0.72 1.9 4.4
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 1.85 31.35 44882 2339 99.03 0.17774 0.17545 0.1843 0.22222 0.227 RANDOM 22.21
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] 0.57 -0.85 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.405 r_dihedral_angle_4_deg 20.173 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 5.146 r_angle_refined_deg 1.775 r_angle_other_deg 1.276 r_symmetry_vdw_refined 0.342 r_nbd_refined 0.267 r_symmetry_vdw_other 0.237 r_nbd_other 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.405 r_dihedral_angle_4_deg 20.173 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 5.146 r_angle_refined_deg 1.775 r_angle_other_deg 1.276 r_symmetry_vdw_refined 0.342 r_nbd_refined 0.267 r_symmetry_vdw_other 0.237 r_nbd_other 0.222 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.109 r_nbtor_other 0.1 r_metal_ion_refined 0.085 r_xyhbond_nbd_other 0.076 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.007 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 4086 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing