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PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000464a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHK 1YHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 80 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.017 α = 90 b = 58.017 β = 90 c = 395.554 γ = 120
Symmetry Space Group P 61 2 2
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 PILATUS 6M-F 2017-10-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.41 197.85 100 0.095 0.098 0.024 0.996 13.1 15.5 78228
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 1.41 1.45 100 1.992 2.104 0.67 0.549 9.6 5638
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 FOURIER SYNTHESIS THROUGHOUT 1YHK 1.41 65.93 73370 4007 99.03 0.1983 0.1966 0.2098 0.2282 0.2403 RANDOM 22.554
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 0.11 0.22 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.962 r_dihedral_angle_4_deg 17.164 r_dihedral_angle_3_deg 15.092 r_dihedral_angle_1_deg 5.797 r_mcangle_it 2.547 r_angle_refined_deg 2.44 r_mcbond_other 1.896 r_mcbond_it 1.871 r_angle_other_deg 1.171 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.962 r_dihedral_angle_4_deg 17.164 r_dihedral_angle_3_deg 15.092 r_dihedral_angle_1_deg 5.797 r_mcangle_it 2.547 r_angle_refined_deg 2.44 r_mcbond_other 1.896 r_mcbond_it 1.871 r_angle_other_deg 1.171 r_chiral_restr 0.146 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2871 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing