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Structure of Leucyl aminopeptidase from Trypanosoma cruzi in complex with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Phosphate-citrate pH 4.2, 40 % (v/v) PEG 300, 5 mM MnSO4, 5 mM amastatin
Crystal Properties Matthews coefficient Solvent content 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.12 α = 90 b = 160.12 β = 90 c = 203.672 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 PIXEL DECTRIS PILATUS 6M-F 2014-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.32 57.31 100 0.188 11 11 43546
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.4 100 1.202 11.1
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 MOLECULAR REPLACEMENT THROUGHOUT 5NSK 2.32 57.31 41361 2183 99.98 0.16772 0.16552 0.1747 0.20997 0.2125 RANDOM 31.21
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] -1.73 -0.86 -1.73 5.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.266 r_dihedral_angle_3_deg 14.892 r_dihedral_angle_4_deg 13.011 r_dihedral_angle_1_deg 6.527 r_long_range_B_other 5.661 r_long_range_B_refined 5.66 r_scangle_other 4.036 r_mcangle_it 2.768 r_mcangle_other 2.767 r_scbond_it 2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.266 r_dihedral_angle_3_deg 14.892 r_dihedral_angle_4_deg 13.011 r_dihedral_angle_1_deg 6.527 r_long_range_B_other 5.661 r_long_range_B_refined 5.66 r_scangle_other 4.036 r_mcangle_it 2.768 r_mcangle_other 2.767 r_scbond_it 2.551 r_scbond_other 2.535 r_mcbond_it 1.741 r_mcbond_other 1.74 r_angle_refined_deg 1.544 r_angle_other_deg 1.258 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7610 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing