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Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M and E75A mutants) from the Wild Tomato Solanum habrochaites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 291 70% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Tris, pH 8.0.
Crystal Properties Matthews coefficient Solvent content 2.18 43.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.891 α = 90 b = 51.891 β = 90 c = 173.286 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315r 2013-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.05 25 97.4 0.044 52.3 11 15386
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 2.05 2.12 94.6 0.495 4.3 10
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 MOLECULAR REPLACEMENT THROUGHOUT 1JP3 2.05 23.22 14337 751 95.95 0.19413 0.19163 0.2002 0.24135 0.2484 RANDOM 28.296
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_3_deg 15.894 r_dihedral_angle_4_deg 13.301 r_dihedral_angle_1_deg 5.659 r_long_range_B_refined 5.261 r_long_range_B_other 4.9 r_scangle_other 2.835 r_mcangle_it 2.25 r_mcangle_other 2.249 r_scbond_it 1.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_3_deg 15.894 r_dihedral_angle_4_deg 13.301 r_dihedral_angle_1_deg 5.659 r_long_range_B_refined 5.261 r_long_range_B_other 4.9 r_scangle_other 2.835 r_mcangle_it 2.25 r_mcangle_other 2.249 r_scbond_it 1.696 r_scbond_other 1.696 r_mcbond_other 1.35 r_mcbond_it 1.349 r_angle_refined_deg 1.159 r_angle_other_deg 0.735 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1771 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing