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Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic 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 2.55 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.308 α = 90 b = 91.568 β = 94.37 c = 106.871 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 273 CCD MARRESEARCH SX-165 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 2.4 33 99.7 0.1 9.7 3.6 77588 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 2.4 2.53 99.4 0.48 2.6 3.6
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 2.4 32.43 73667 3901 99.67 0.20265 0.19948 0.196 0.26225 0.2558 RANDOM 26.566
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] -1.45 1.27 2.04 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_4_deg 13.914 r_dihedral_angle_1_deg 6.261 r_scangle_it 1.968 r_angle_refined_deg 1.244 r_scbond_it 1.203 r_mcangle_it 0.775 r_mcbond_it 0.439 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_4_deg 13.914 r_dihedral_angle_1_deg 6.261 r_scangle_it 1.968 r_angle_refined_deg 1.244 r_scbond_it 1.203 r_mcangle_it 0.775 r_mcbond_it 0.439 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 13391 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement