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Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with IPP
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 6.5 291 13% PEG 10K, 20mM 18-crown-6, 0.1M MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.311 α = 90 b = 64.545 β = 90 c = 127.156 γ = 90
Symmetry Space Group P 21 21 21
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 315 2015-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.95 25 99.7 0.041 33 4 35453
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 1.95 2.02 100 0.54 3 4.1
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 1.95 25 33319 1761 98.38 0.20134 0.19916 0.2078 0.243 0.2481 RANDOM 23.525
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 0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.838 r_dihedral_angle_4_deg 16.293 r_dihedral_angle_3_deg 15.167 r_dihedral_angle_1_deg 6.451 r_long_range_B_refined 4.858 r_long_range_B_other 4.858 r_scangle_other 2.6 r_mcangle_it 2.058 r_mcangle_other 2.058 r_scbond_it 1.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.838 r_dihedral_angle_4_deg 16.293 r_dihedral_angle_3_deg 15.167 r_dihedral_angle_1_deg 6.451 r_long_range_B_refined 4.858 r_long_range_B_other 4.858 r_scangle_other 2.6 r_mcangle_it 2.058 r_mcangle_other 2.058 r_scbond_it 1.591 r_scbond_other 1.59 r_angle_refined_deg 1.345 r_mcbond_it 1.249 r_mcbond_other 1.243 r_angle_other_deg 1.219 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 3587 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing