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Structure of Leucyl aminopeptidase from Leishmania major 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 0.8 M Succinic acid pH 7.0, 3 % (w/v) 1,5-Diamino-pentane di-hydrochloride, 5 mM MnSO4, 5 mM actinonin
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.439 α = 90 b = 116.439 β = 90 c = 91.491 γ = 120
Symmetry Space Group P 3 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 100 PIXEL DECTRIS PILATUS 6M 2013-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97781 Diamond I24
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 2.5 38.11 87.8 0.15 8.2 5.7 21850
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 2.5 2.6 90.2 0.747 2 5.6
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 2.5 38.11 20818 1031 86.72 0.19649 0.19397 0.1998 0.24486 0.2497 RANDOM 32.765
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] -1.71 -0.85 -1.71 5.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.313 r_dihedral_angle_4_deg 17.932 r_dihedral_angle_3_deg 16.235 r_dihedral_angle_1_deg 6.993 r_long_range_B_refined 4.187 r_long_range_B_other 4.187 r_scangle_other 2.614 r_mcangle_it 2.474 r_mcangle_other 2.473 r_scbond_it 1.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.313 r_dihedral_angle_4_deg 17.932 r_dihedral_angle_3_deg 16.235 r_dihedral_angle_1_deg 6.993 r_long_range_B_refined 4.187 r_long_range_B_other 4.187 r_scangle_other 2.614 r_mcangle_it 2.474 r_mcangle_other 2.473 r_scbond_it 1.726 r_scbond_other 1.726 r_angle_refined_deg 1.642 r_mcbond_it 1.459 r_mcbond_other 1.456 r_angle_other_deg 1 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 3893 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing