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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, HANGING DROP 4.2 295 0.1 M phosphate/citrate buffer, pH 4.2, 40 % PEG 300
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.644 α = 90 b = 53.695 β = 90 c = 102.33 γ = 90
Symmetry Space Group P 21 21 21
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 6M-F 2012-09-28 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.969 Diamond I02
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 1.7 51.17 95.7 11.9 3.2 25369
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 1.7 1.73 89.3 1.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 51.17 14932 812 95.41 0.20715 0.20469 0.25137 0.2329 RANDOM 14.788
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] -0.19 1.05 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.987 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_4_deg 13.293 r_dihedral_angle_1_deg 7.152 r_long_range_B_refined 5.034 r_long_range_B_other 4.784 r_scangle_other 2.617 r_angle_refined_deg 1.869 r_scbond_it 1.7 r_mcangle_it 1.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.987 r_dihedral_angle_3_deg 14.359 r_dihedral_angle_4_deg 13.293 r_dihedral_angle_1_deg 7.152 r_long_range_B_refined 5.034 r_long_range_B_other 4.784 r_scangle_other 2.617 r_angle_refined_deg 1.869 r_scbond_it 1.7 r_mcangle_it 1.662 r_mcangle_other 1.662 r_scbond_other 1.62 r_mcbond_it 1.047 r_mcbond_other 1.043 r_angle_other_deg 0.82 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1746 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement