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Novel bacterial methionine aminopeptidase inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GG2 PDB ENTRY 2GG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, batch, pH 7.0, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.045 α = 90 b = 62.744 β = 108.85 c = 52.667 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 2 1
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 1.45 24.92 96.4 0.031 18.7 2.5 40960 40960
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) 1.45 1.55 85.3 0.235 4.23 1.2 6408
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 2GG2 1.45 24.92 40960 40960 2076 96.38 0.126 0.124 0.124 0.1243 0.161 0.1613 RANDOM 15.946
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] -0.41 0.45 0.42 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.106 r_dihedral_angle_4_deg 19.284 r_sphericity_free 12.261 r_dihedral_angle_3_deg 12.055 r_scangle_it 6.24 r_dihedral_angle_1_deg 6.08 r_sphericity_bonded 5.828 r_scbond_it 4.414 r_mcangle_it 2.967 r_rigid_bond_restr 2.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.106 r_dihedral_angle_4_deg 19.284 r_sphericity_free 12.261 r_dihedral_angle_3_deg 12.055 r_scangle_it 6.24 r_dihedral_angle_1_deg 6.08 r_sphericity_bonded 5.828 r_scbond_it 4.414 r_mcangle_it 2.967 r_rigid_bond_restr 2.098 r_mcbond_it 2.084 r_angle_refined_deg 1.719 r_mcbond_other 1.168 r_angle_other_deg 0.744 r_symmetry_vdw_other 0.383 r_symmetry_vdw_refined 0.253 r_symmetry_hbond_refined 0.249 r_nbd_refined 0.217 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.178 r_chiral_restr 0.091 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.069 r_metal_ion_refined 0.044 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection SCALEPACK data scaling AMoRE phasing