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Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W8Q PDB ENTRY 1W8Q
Crystallization Crystal Properties Matthews coefficient Solvent content 2.39 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.123 α = 90 b = 90.692 β = 94.52 c = 105.729 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.2 35.25 99.5 0.09 12.1 5.4 97096
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 2.2 2.32 99.1 0.47 3.3 5.5
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 1W8Q 2.2 35.25 92157 4878 99.27 0.209 0.20631 0.2065 0.26035 0.2087 RANDOM 35.646
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.696 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 14.882 r_dihedral_angle_1_deg 5.964 r_scangle_it 2.556 r_scbond_it 1.527 r_angle_refined_deg 1.217 r_mcangle_it 1.026 r_mcbond_it 0.545 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.696 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 14.882 r_dihedral_angle_1_deg 5.964 r_scangle_it 2.556 r_scbond_it 1.527 r_angle_refined_deg 1.217 r_mcangle_it 1.026 r_mcbond_it 0.545 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 13351 Nucleic Acid Atoms Solvent Atoms 1073 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling