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Novel bacterial methionine aminopeptidase inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GG0 PDB ENTRY 2GG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 7 298 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.87 34.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.754 α = 90 b = 59.468 β = 111.64 c = 51.197 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 CCD ADSC QUANTUM 4 2002-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1 23.8 93.2 0.021 28.1 2.6 98330 98330
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 1.15 73.2 0.082 11.2 1.5 17489
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2GG0 1 23.8 98330 98330 4955 84.55 0.12 0.12 0.12 0.1285 0.133 0.1387 RANDOM 8.287
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] 0.09 -0.02 0.11 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.742 r_dihedral_angle_4_deg 13.369 r_dihedral_angle_3_deg 12.713 r_dihedral_angle_1_deg 8.467 r_sphericity_free 6.205 r_scangle_it 3.567 r_sphericity_bonded 2.655 r_scbond_it 2.411 r_mcangle_it 1.928 r_angle_refined_deg 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.742 r_dihedral_angle_4_deg 13.369 r_dihedral_angle_3_deg 12.713 r_dihedral_angle_1_deg 8.467 r_sphericity_free 6.205 r_scangle_it 3.567 r_sphericity_bonded 2.655 r_scbond_it 2.411 r_mcangle_it 1.928 r_angle_refined_deg 1.39 r_mcbond_it 1.238 r_rigid_bond_restr 1.026 r_angle_other_deg 0.718 r_mcbond_other 0.563 r_symmetry_hbond_refined 0.367 r_nbd_refined 0.343 r_symmetry_vdw_refined 0.318 r_symmetry_vdw_other 0.309 r_nbd_other 0.225 r_xyhbond_nbd_refined 0.218 r_metal_ion_refined 0.187 r_nbtor_refined 0.177 r_xyhbond_nbd_other 0.105 r_nbtor_other 0.088 r_chiral_restr 0.083 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2311 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction