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Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Actinonin
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 Tris pH 8.0, 2.4 M (NH4)2SO4, 5 mM MnSO4, 5 mM actinonin
Crystal Properties Matthews coefficient Solvent content 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.909 α = 90 b = 165.73 β = 112.45 c = 121.98 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2013-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
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 3 41.5 97 0.116 4.5 3.2 68219
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 3 3.07 98 0.44 2 3.2 4424
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NSK 3 41.5 63948 3327 95.52 0.26617 0.26464 0.29641 0.2803 RANDOM 35.895
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] 1.08 0.22 -3.67 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.439 r_dihedral_angle_3_deg 14.316 r_dihedral_angle_4_deg 12.986 r_long_range_B_refined 6.16 r_long_range_B_other 6.16 r_dihedral_angle_1_deg 6.039 r_mcangle_it 4.593 r_mcangle_other 4.593 r_scangle_other 3.632 r_mcbond_it 2.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.439 r_dihedral_angle_3_deg 14.316 r_dihedral_angle_4_deg 12.986 r_long_range_B_refined 6.16 r_long_range_B_other 6.16 r_dihedral_angle_1_deg 6.039 r_mcangle_it 4.593 r_mcangle_other 4.593 r_scangle_other 3.632 r_mcbond_it 2.773 r_mcbond_other 2.772 r_scbond_it 2.087 r_scbond_other 2.087 r_angle_refined_deg 1.443 r_angle_other_deg 1.254 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 22467 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing