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Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BGX PDB ENTRY 2BGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 1M LiCl, 10 % PEG 6K, 0.1M ZnCl2, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.41 63.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.274 α = 90 b = 88.274 β = 90 c = 181.834 γ = 120
Symmetry Space Group P 61 2 2
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 2007-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.978850 ESRF BM30A
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 1.75 47.5 98.6 0.079 28.6 17 42426
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 1.75 1.84 92.7 0.825 2.2 7.1 5643
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BGX 1.75 44.15 40210 2136 98.38 0.20919 0.2069 0.2066 0.25326 0.2536 RANDOM 12.923
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] -0.26 -0.13 -0.26 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.9 r_dihedral_angle_3_deg 16.669 r_dihedral_angle_4_deg 15.663 r_dihedral_angle_1_deg 6.582 r_scangle_it 3.924 r_mcangle_it 3.197 r_scbond_it 2.799 r_mcbond_it 2.509 r_angle_refined_deg 1.494 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.9 r_dihedral_angle_3_deg 16.669 r_dihedral_angle_4_deg 15.663 r_dihedral_angle_1_deg 6.582 r_scangle_it 3.924 r_mcangle_it 3.197 r_scbond_it 2.799 r_mcbond_it 2.509 r_angle_refined_deg 1.494 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2098 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing