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Structure of the M1 Alanylaminopeptidase from malaria complexed with the phosphinate dipeptide analog
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 22% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris (pH 8.5), 0.2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.852 α = 90 b = 108.633 β = 90 c = 118.325 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 CCD MAR CCD 165 mm 2008-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.65 108.605 83.2 0.064 0.064 8.673 2.8 57395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 74.6 0.369 0.369 1.8 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 28.61 57395 3078 90.67 0.17729 0.17495 0.1745 0.22132 0.2202 RANDOM 14.542
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] -1.24 -1 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.702 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 5.904 r_scangle_it 4.412 r_scbond_it 3.14 r_mcangle_it 1.794 r_angle_refined_deg 1.331 r_mcbond_it 1.201 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.702 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 5.904 r_scangle_it 4.412 r_scbond_it 3.14 r_mcangle_it 1.794 r_angle_refined_deg 1.331 r_mcbond_it 1.201 r_nbtor_refined 0.297 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.118 r_metal_ion_refined 0.093 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7291 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 60
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction