☰ Navigation Tabs
Crystal Structure of T. cruzi FPPS after initial refinement with no ligand modelled (structure $n)
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 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.681 α = 90 b = 57.681 β = 90 c = 396.512 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 2017-10-08 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 1.62 132.19 100 0.1 0.103 0.024 0.999 15 17.7 51799
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 1.62 1.66 100 2.734 2.831 0.73 0.523 14.9 3733
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 1.62 66.09 48589 2650 99.15 0.1934 0.1916 0.2021 0.2274 0.2339 RANDOM 30.73
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.017 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 5.36 r_mcangle_it 3.673 r_mcbond_it 2.729 r_mcbond_other 2.728 r_angle_refined_deg 2.015 r_angle_other_deg 1.103 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.017 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 5.36 r_mcangle_it 3.673 r_mcbond_it 2.729 r_mcbond_other 2.728 r_angle_refined_deg 2.015 r_angle_other_deg 1.103 r_chiral_restr 0.125 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2871 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing