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Crystal structure of Serratia marcescens L-Ala D-Glu endopeptidase ChiX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M tris HCl pH 7.5
0.14 M trimethylamine-N-oxide
16% (w/v) polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 1.95 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.627 α = 90 b = 55.531 β = 90 c = 51.78 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 PIXEL DECTRIS PILATUS3 S 6M 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.977 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.34 55.53 90.5 0.084 0.052 0.998 6.7 6.9 50019 6.877
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.36 50.4 0.523 0.34 0.829 2.3 6.1
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 THROUGHOUT 1.34 51.78 47549 2470 96.64 0.09083 0.08921 0.12013 0.1201 RANDOM 11.119
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] 0.04 0.07 -0.17 0.13
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.586 r_dihedral_angle_2_deg 24.648 r_dihedral_angle_4_deg 19.375 r_dihedral_angle_3_deg 13.799 r_sphericity_bonded 8.258 r_dihedral_angle_1_deg 5.839 r_long_range_B_refined 3.235 r_long_range_B_other 2.571 r_scangle_other 1.974 r_angle_refined_deg 1.659
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.586 r_dihedral_angle_2_deg 24.648 r_dihedral_angle_4_deg 19.375 r_dihedral_angle_3_deg 13.799 r_sphericity_bonded 8.258 r_dihedral_angle_1_deg 5.839 r_long_range_B_refined 3.235 r_long_range_B_other 2.571 r_scangle_other 1.974 r_angle_refined_deg 1.659 r_scbond_it 1.57 r_scbond_other 1.569 r_rigid_bond_restr 1.491 r_angle_other_deg 1.388 r_mcangle_it 1.383 r_mcangle_other 1.383 r_mcbond_it 1.075 r_mcbond_other 1.071 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2136 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing