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Crystal structure of T. cruzi GPX1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5R Homology model based on 2P5R, all loops deleted
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.9 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.846 α = 90 b = 46.591 β = 121.54 c = 61.163 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 31.47 94.1 7987 7515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 85.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Homology model based on 2P5R, all loops deleted 2.3 25.42 7155 349 94.07 0.20951 0.20739 0.2077 0.25368 RANDOM 49.509
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] 0.35 0.46 -0.13 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.526 r_dihedral_angle_3_deg 19.448 r_dihedral_angle_4_deg 17.943 r_dihedral_angle_1_deg 5.557 r_mcangle_it 2.745 r_scangle_it 2.481 r_angle_refined_deg 1.933 r_scbond_it 1.812 r_mcbond_it 1.802 r_symmetry_vdw_refined 0.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.526 r_dihedral_angle_3_deg 19.448 r_dihedral_angle_4_deg 17.943 r_dihedral_angle_1_deg 5.557 r_mcangle_it 2.745 r_scangle_it 2.481 r_angle_refined_deg 1.933 r_scbond_it 1.812 r_mcbond_it 1.802 r_symmetry_vdw_refined 0.348 r_nbtor_refined 0.339 r_nbd_refined 0.301 r_xyhbond_nbd_refined 0.289 r_chiral_restr 0.159 r_symmetry_hbond_refined 0.107 r_bond_refined_d 0.021 r_gen_planes_refined 0.021 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1194 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing