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1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Lithium Sulfate, 0.1 M Tris:HCl pH 8.5, 1.26 M Ammonium Sulfate, 0.05 M DMSO
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.767 α = 90 b = 88.644 β = 90 c = 133.402 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 PILATUS3 S 6M Double Crystal 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9795 APS 19-ID
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 1.3 40 99.4 0.08 22 7.4 217263
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 1.3 1.32
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 1.3 40 176526 9439 95.2 0.11497 0.113 0.1135 0.15254 0.1528 RANDOM 18.628
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] 0.12 -0.17 0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.399 r_dihedral_angle_2_deg 35.703 r_dihedral_angle_4_deg 17.956 r_sphericity_bonded 16.081 r_dihedral_angle_3_deg 12.639 r_scangle_other 6.626 r_long_range_B_refined 6.391 r_dihedral_angle_1_deg 6.122 r_scbond_other 6.071 r_scbond_it 6.068
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.399 r_dihedral_angle_2_deg 35.703 r_dihedral_angle_4_deg 17.956 r_sphericity_bonded 16.081 r_dihedral_angle_3_deg 12.639 r_scangle_other 6.626 r_long_range_B_refined 6.391 r_dihedral_angle_1_deg 6.122 r_scbond_other 6.071 r_scbond_it 6.068 r_rigid_bond_restr 5.749 r_long_range_B_other 5.566 r_mcbond_other 2.867 r_mcbond_it 2.866 r_mcangle_it 2.863 r_mcangle_other 2.863 r_angle_refined_deg 2.435 r_angle_other_deg 1.322 r_chiral_restr 0.179 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 5736 Nucleic Acid Atoms Solvent Atoms 1129 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing