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unliganded Structure of Leucyl aminopeptidase from Trypanosoma brucei
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 6.8, 0.2 M MgCl2, 11 % (w/v) PEG 8000, 10 microM ZnCl2, 10 mM L-leucine
Crystal Properties Matthews coefficient Solvent content 2.54 51.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.368 α = 90 b = 143.76 β = 95.47 c = 270.085 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 6M-F 2014-04-27 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 2.4 32.73 94.5 0.117 5.7 3.3 244412
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 2.4 2.44 88.7 0.351 2 2.9 11362
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 2.4 32.73 232199 11981 94.27 0.20689 0.20595 0.208 0.22508 0.2261 RANDOM 34.619
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] 3.46 -1.16 -1.65 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.511 r_dihedral_angle_4_deg 15.568 r_dihedral_angle_3_deg 13.544 r_dihedral_angle_1_deg 5.884 r_long_range_B_refined 4.434 r_long_range_B_other 4.407 r_scangle_other 3.112 r_mcangle_it 2.664 r_mcangle_other 2.664 r_angle_other_deg 2.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.511 r_dihedral_angle_4_deg 15.568 r_dihedral_angle_3_deg 13.544 r_dihedral_angle_1_deg 5.884 r_long_range_B_refined 4.434 r_long_range_B_other 4.407 r_scangle_other 3.112 r_mcangle_it 2.664 r_mcangle_other 2.664 r_angle_other_deg 2.323 r_scbond_it 1.938 r_scbond_other 1.934 r_mcbond_it 1.673 r_mcbond_other 1.673 r_angle_refined_deg 1.397 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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 45554 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing