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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 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.131 α = 90 b = 63.29 β = 109.71 c = 52.513 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 1.05 25.68 99.7 0.022 23.5 2.9 111880 111880
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) 1.05 1.15 99.4 0.137 10.9 1.6 26528
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 1.05 25.68 111871 111871 5600 99.76 0.141 0.14 0.14 0.1492 0.159 0.1673 RANDOM 12.426
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] 0.05 0.32 0.22 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.239 r_dihedral_angle_4_deg 17.38 r_dihedral_angle_3_deg 11.665 r_sphericity_free 9.461 r_dihedral_angle_1_deg 6.607 r_sphericity_bonded 5.686 r_scangle_it 4.645 r_scbond_it 3.198 r_mcangle_it 2.436 r_mcbond_it 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.239 r_dihedral_angle_4_deg 17.38 r_dihedral_angle_3_deg 11.665 r_sphericity_free 9.461 r_dihedral_angle_1_deg 6.607 r_sphericity_bonded 5.686 r_scangle_it 4.645 r_scbond_it 3.198 r_mcangle_it 2.436 r_mcbond_it 1.67 r_rigid_bond_restr 1.557 r_angle_refined_deg 1.539 r_mcbond_other 1.081 r_angle_other_deg 0.783 r_symmetry_vdw_refined 0.427 r_symmetry_vdw_other 0.346 r_symmetry_hbond_refined 0.284 r_nbd_refined 0.221 r_chiral_restr 0.213 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.193 r_nbtor_refined 0.177 r_metal_ion_refined 0.151 r_nbtor_other 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2176 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection SCALEPACK data scaling AMoRE phasing