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Crystal structure of Trypanosoma cruzi formiminoglutamase with Mn2+2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A0M PDB ENTRY 2A0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 294 A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2, 1 mM TCEP] was mixed with a 4 UL drop of precipitant solution [31% PEG 300, 0.1 M sodium acetate (pH 4.9)] on a siliconized cover slide and equilibrated against a 500 UL reservoir of precipitant solution at 294K. The yielded crystal is apo. To obtain the Mn2+2 bound form, this apo-crystal was soaked with 5 mM MnCl2 in 0.1 M sodium malonate (pH 8.0), 27% PEG 3350) for 24 hours, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.922 α = 90 b = 128.922 β = 90 c = 85.377 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2013-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 50 99.2 0.059 0.059 14.162 2.5 44906 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 98.8 0.438 0.438 2.013 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 2A0M 1.849 21.964 0.06 44906 42190 2123 93.23 0.1882 0.1865 0.1871 0.2169 0.2135 random
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] -1.9726 -1.9726 4.0766
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.737 f_angle_d 0.795 f_chiral_restr 0.059 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4552 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 10
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling