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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 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 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.123 α = 90 b = 62.945 β = 109.01 c = 52.743 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 1.12 23.98 93.2 0.021 28.1 2.6 91914 91914
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) 1.12 1.25 73.2 0.082 11.2 1.5 25659
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 1.12 23.98 91867 91867 4597 99.14 0.133 0.132 0.132 0.1417 0.155 0.1644 RANDOM 11.436
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] -0.22 0.24 0.38 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 11.581 r_sphericity_free 9.599 r_dihedral_angle_1_deg 6.013 r_sphericity_bonded 5.375 r_scangle_it 4.354 r_scbond_it 3.001 r_mcangle_it 2.27 r_angle_refined_deg 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.559 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 11.581 r_sphericity_free 9.599 r_dihedral_angle_1_deg 6.013 r_sphericity_bonded 5.375 r_scangle_it 4.354 r_scbond_it 3.001 r_mcangle_it 2.27 r_angle_refined_deg 1.64 r_mcbond_it 1.585 r_rigid_bond_restr 1.483 r_mcbond_other 1.053 r_angle_other_deg 0.727 r_symmetry_vdw_other 0.372 r_nbd_refined 0.229 r_nbd_other 0.193 r_symmetry_hbond_refined 0.186 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.164 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2224 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection SCALEPACK data scaling AMoRE phasing