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Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with DMSPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HXN
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 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.752 α = 90 b = 66.8 β = 90 c = 128.726 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 2015-01-22 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 99.3 0.043 42.4 5.9 38064
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 99.8 0.76 5.7
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 5HXN 1.95 25 31779 1679 87.28 0.1964 0.19397 0.2025 0.24128 0.2446 RANDOM 30.882
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] -0.46 1.26 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.174 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_4_deg 13.638 r_long_range_B_refined 5.844 r_long_range_B_other 5.561 r_dihedral_angle_1_deg 5.529 r_scangle_other 3.085 r_mcangle_other 2.467 r_mcangle_it 2.466 r_scbond_it 1.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.174 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_4_deg 13.638 r_long_range_B_refined 5.844 r_long_range_B_other 5.561 r_dihedral_angle_1_deg 5.529 r_scangle_other 3.085 r_mcangle_other 2.467 r_mcangle_it 2.466 r_scbond_it 1.844 r_scbond_other 1.844 r_mcbond_it 1.479 r_mcbond_other 1.477 r_angle_refined_deg 1.246 r_angle_other_deg 1.129 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.003 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 3639 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling