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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 INHIBITOR SOLUTION.
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.297 α = 90 b = 65.297 β = 90 c = 134.779 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 2.5 50 96.8 0.08 16.9 4.2 18900 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 2.5 2.65 90.1 0.28 5.8 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3UAG 2.5 46.18 18383 939 99 0.195 0.192 0.261 0.233 RANDOM 15.35
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.244 r_dihedral_angle_4_deg 17.326 r_dihedral_angle_3_deg 12.629 r_scangle_it 5.457 r_scbond_it 3.501 r_dihedral_angle_1_deg 3.101 r_mcangle_it 2.058 r_angle_refined_deg 1.415 r_mcbond_it 1.163 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.244 r_dihedral_angle_4_deg 17.326 r_dihedral_angle_3_deg 12.629 r_scangle_it 5.457 r_scbond_it 3.501 r_dihedral_angle_1_deg 3.101 r_mcangle_it 2.058 r_angle_refined_deg 1.415 r_mcbond_it 1.163 r_nbtor_refined 0.32 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.217 r_symmetry_hbond_refined 0.209 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 3228 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing