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The crystal structure of UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (MPL) from Neisseria meningitides
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.1M MES, 12% PEG20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.75 55.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.497 α = 90 b = 83.8 β = 90 c = 143.838 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 CCD ADSC QUANTUM 315 2008-04-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 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 2.55 50 99.8 0.111 21.8 7 26427 26374 55.5
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 2.55 2.57 97.3 0.908 1.83 6.1 613
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.55 50 26315 26315 1331 99.58 0.18623 0.18623 0.18324 0.1818 0.24255 0.2398 RANDOM 43.959
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] 2.91 -1.45 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.265 r_dihedral_angle_4_deg 18.302 r_dihedral_angle_3_deg 16.879 r_dihedral_angle_1_deg 6.097 r_scangle_it 2.806 r_scbond_it 1.756 r_angle_refined_deg 1.47 r_mcangle_it 1.23 r_mcbond_it 0.697 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.265 r_dihedral_angle_4_deg 18.302 r_dihedral_angle_3_deg 16.879 r_dihedral_angle_1_deg 6.097 r_scangle_it 2.806 r_scbond_it 1.756 r_angle_refined_deg 1.47 r_mcangle_it 1.23 r_mcbond_it 0.697 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.292 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4953 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 12
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling