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Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WK0 PDB ENTRY 2WK0
Crystallization Crystal Properties Matthews coefficient Solvent content 2.67 53.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.898 α = 90 b = 92.348 β = 92.25 c = 143.829 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH SX-165 2010-01-25 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 2.8 38.8 99.4 0.08 12.7 3.5 49784 2
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 2.8 2.95 99.5 0.43 2.6 3.5
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 2WK0 2.8 27.53 47215 2527 99.3 0.219 0.217 0.2164 0.264 0.2627 RANDOM 48.76
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] -0.08 -0.06 0.19 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.633 r_dihedral_angle_3_deg 18.362 r_dihedral_angle_4_deg 13.903 r_dihedral_angle_1_deg 5.656 r_angle_refined_deg 1.164 r_scangle_it 0.898 r_scbond_it 0.567 r_mcangle_it 0.458 r_nbtor_refined 0.302 r_mcbond_it 0.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.633 r_dihedral_angle_3_deg 18.362 r_dihedral_angle_4_deg 13.903 r_dihedral_angle_1_deg 5.656 r_angle_refined_deg 1.164 r_scangle_it 0.898 r_scbond_it 0.567 r_mcangle_it 0.458 r_nbtor_refined 0.302 r_mcbond_it 0.259 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.209 r_metal_ion_refined 0.186 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.074 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_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 13390 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing