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Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UAG PDB ENTRY 3UAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN WAS CRYSTALLIZED FROM 1.7 M (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 2 MM OF INHIBITOR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.288 α = 90 b = 65.288 β = 90 c = 135.06 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 288 CCD ADSC CCD 2006-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.89 50 97.9 0.06 22 4.9 44144 3
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 1.89 2 93.6 0.29 6 4.9
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 3UAG 1.89 46.18 42746 2256 99.7 0.175 0.173 0.1728 0.215 0.2144 RANDOM 18.8
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] 0.3 0.3 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.785 r_dihedral_angle_4_deg 15.421 r_dihedral_angle_3_deg 12.518 r_dihedral_angle_1_deg 5.945 r_scangle_it 3.44 r_scbond_it 2.161 r_angle_refined_deg 1.366 r_mcangle_it 1.362 r_mcbond_it 0.884 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.785 r_dihedral_angle_4_deg 15.421 r_dihedral_angle_3_deg 12.518 r_dihedral_angle_1_deg 5.945 r_scangle_it 3.44 r_scbond_it 2.161 r_angle_refined_deg 1.366 r_mcangle_it 1.362 r_mcbond_it 0.884 r_nbtor_refined 0.297 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3253 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing