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Structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 21%(v/v) 2-propanl, 30% (v/v) Glyceol 0.07M sodium cacodylate trihydrate pH 6.5, 0.14M Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 4 69.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.96 α = 90 b = 119.96 β = 90 c = 116.73 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 104.15 PIXEL DECTRIS EIGER X 9M 2020-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97949 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.48 29.18 100 0.023 20.4 17.7 30793
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.57 0.424
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4BUB 2.48 20.001 30729 1983 99.727 0.23 0.2281 0.2289 0.2598 0.2629 28.554
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] -0.002 -0.002 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.061 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 16.068 r_lrange_it 6.481 r_lrange_other 6.48 r_dihedral_angle_1_deg 6.25 r_scangle_it 6.038 r_scangle_other 6.037 r_scbond_it 4.478 r_scbond_other 4.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.061 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 16.068 r_lrange_it 6.481 r_lrange_other 6.48 r_dihedral_angle_1_deg 6.25 r_scangle_it 6.038 r_scangle_other 6.037 r_scbond_it 4.478 r_scbond_other 4.477 r_mcangle_it 4.135 r_mcangle_other 4.135 r_mcbond_it 3.043 r_mcbond_other 3.041 r_angle_other_deg 2.325 r_angle_refined_deg 1.776 r_symmetry_nbd_refined 0.284 r_nbd_other 0.267 r_symmetry_nbd_other 0.236 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.211 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.184 r_symmetry_xyhbond_nbd_other 0.114 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.08 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3796 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxDC data collection XDS data scaling PHENIX phasing