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Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase with D71M, E75A and H103Y Mutants
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 VAPOR DIFFUSION 7 291 5% (w/v) PEG 8000, 40% MPD, 0.1 M Cacodylate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.16 43.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.683 α = 90 b = 51.683 β = 90 c = 173.561 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 210 2014-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0 SPring-8 BL12B2
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 99.9 0.043 42.8 10.6 15682
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 99.9 0.412 9.6
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 24.78 14812 777 99.77 0.19338 0.19113 0.2007 0.23646 0.2413 RANDOM 27.691
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.221 r_dihedral_angle_4_deg 15.356 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_1_deg 5.868 r_long_range_B_refined 5.02 r_long_range_B_other 4.876 r_scangle_other 2.999 r_mcangle_it 2.271 r_mcangle_other 2.27 r_scbond_it 1.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.221 r_dihedral_angle_4_deg 15.356 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_1_deg 5.868 r_long_range_B_refined 5.02 r_long_range_B_other 4.876 r_scangle_other 2.999 r_mcangle_it 2.271 r_mcangle_other 2.27 r_scbond_it 1.823 r_scbond_other 1.822 r_mcbond_it 1.387 r_mcbond_other 1.387 r_angle_refined_deg 1.214 r_angle_other_deg 0.743 r_chiral_restr 0.066 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 1755 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing