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apo Structure of Leucyl aminopeptidase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HB6 2HB6 poly-Ala model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.8 M Na citrate pH 7.0, 5 mM CoSO4
Crystal Properties Matthews coefficient Solvent content 3.51 64.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.33 α = 90 b = 162.45 β = 90 c = 176.99 γ = 90
Symmetry Space Group P 21 21 21
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 2.6 72.61 100 0.165 9.5 7.4 143992
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 2.6 2.64 100 1.019 2 7.5 7106
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 2HB6 poly-Ala model 2.6 72.61 136637 7257 99.99 0.19212 0.19113 0.1959 0.21085 0.2129 RANDOM 38.096
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] -1.81 0.71 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.344 r_dihedral_angle_4_deg 20.352 r_dihedral_angle_3_deg 13.692 r_dihedral_angle_1_deg 6.017 r_long_range_B_refined 5.181 r_long_range_B_other 5.169 r_scangle_other 3.593 r_mcangle_it 3.377 r_mcangle_other 3.377 r_scbond_it 2.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.344 r_dihedral_angle_4_deg 20.352 r_dihedral_angle_3_deg 13.692 r_dihedral_angle_1_deg 6.017 r_long_range_B_refined 5.181 r_long_range_B_other 5.169 r_scangle_other 3.593 r_mcangle_it 3.377 r_mcangle_other 3.377 r_scbond_it 2.257 r_scbond_other 2.257 r_mcbond_it 2.076 r_mcbond_other 2.076 r_angle_other_deg 2.006 r_angle_refined_deg 1.532 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 22152 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing