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Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 0.2 M Ammonium chloride, 0.1 M Hepes pH 8, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 345.954 α = 90 b = 42.549 β = 93.07 c = 79.318 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 PIXEL DECTRIS PILATUS 2M 2013-03-11 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.916 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 47.8 98.3 7.8 3.4 47327
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 98.3 1.9 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.8 47.8 27113 1457 97.9 0.276 0.273 0.2736 0.334 0.332 RANDOM 43.86
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] -0.1 1.22 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.416 r_dihedral_angle_3_deg 13.447 r_dihedral_angle_4_deg 8.276 r_dihedral_angle_1_deg 4.794 r_long_range_B_refined 3.649 r_long_range_B_other 3.649 r_mcangle_it 1.702 r_mcangle_other 1.702 r_scangle_other 1.312 r_mcbond_it 0.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.416 r_dihedral_angle_3_deg 13.447 r_dihedral_angle_4_deg 8.276 r_dihedral_angle_1_deg 4.794 r_long_range_B_refined 3.649 r_long_range_B_other 3.649 r_mcangle_it 1.702 r_mcangle_other 1.702 r_scangle_other 1.312 r_mcbond_it 0.952 r_mcbond_other 0.952 r_angle_refined_deg 0.842 r_scbond_it 0.798 r_scbond_other 0.798 r_angle_other_deg 0.677 r_chiral_restr 0.048 r_bond_other_d 0.008 r_bond_refined_d 0.005 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7065 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement