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Crystal structure of farnesyl diphosphate synthase FPPS1 from silkworm, Bombyx mori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 2% Tacsimate pH 5.0, 0.1 M sodium citrate, pH 5.6, 16% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.53 α = 90 b = 64.967 β = 92.425 c = 108.378 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2023-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.8 45.4 99.6 0.133 0.15 0.069 0.993 9.6 4.8 21918
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 0.476 0.542 0.253 0.837
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 42.365 21898 1026 99.491 0.242 0.2398 0.2409 0.2923 0.2936 40.376
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] 1.073 -2.425 0.798 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.82 r_dihedral_angle_3_deg 19.445 r_dihedral_angle_4_deg 13.826 r_lrange_it 6.731 r_dihedral_angle_1_deg 6.004 r_scangle_it 4.249 r_mcangle_it 3.352 r_scbond_it 2.594 r_mcbond_it 2.087 r_angle_refined_deg 1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.82 r_dihedral_angle_3_deg 19.445 r_dihedral_angle_4_deg 13.826 r_lrange_it 6.731 r_dihedral_angle_1_deg 6.004 r_scangle_it 4.249 r_mcangle_it 3.352 r_scbond_it 2.594 r_mcbond_it 2.087 r_angle_refined_deg 1.625 r_nbtor_refined 0.293 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.201 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_refined 0.072 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5494 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing