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Crystal Structure of E. Coli Mur B bound to a Naphthyl Tetronic Acid inihibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MBT PDB entry 1mbt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 25% Polyethyleneglycol 8000, 0.1 M Tris, pH 8.5, 0.1 M Calcium Acetate, Vapor Diffusion, Hanging Drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.993 α = 90 b = 89.301 β = 111.11 c = 50.943 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 IMAGE PLATE RIGAKU RAXIS IV 2003-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 35.87 95.7 12098 11573 1.5 40.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 0.871 1188
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 1mbt 2.51 35.87 11573 964 95.62 0.24 0.166 0.2407 0.244 0.1619 RANDOM 16.352
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] 0.69 0.89 0.09 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.812 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_4_deg 9.983 r_dihedral_angle_1_deg 4.232 r_angle_other_deg 0.729 r_angle_refined_deg 0.722 r_nbtor_refined 0.166 r_nbd_other 0.159 r_nbd_refined 0.148 r_symmetry_vdw_other 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.812 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_4_deg 9.983 r_dihedral_angle_1_deg 4.232 r_angle_other_deg 0.729 r_angle_refined_deg 0.722 r_nbtor_refined 0.166 r_nbd_other 0.159 r_nbd_refined 0.148 r_symmetry_vdw_other 0.11 r_mcangle_it 0.103 r_mcbond_it 0.099 r_nbtor_other 0.078 r_symmetry_hbond_refined 0.073 r_xyhbond_nbd_refined 0.063 r_symmetry_vdw_refined 0.062 r_scangle_it 0.053 r_chiral_restr 0.042 r_scbond_it 0.033 r_mcbond_other 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_refined 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing