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Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product 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 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.16 α = 90 b = 89.16 β = 90 c = 183.64 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 IMAGE PLATE MAR scanner 345 mm plate 2007-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.8 47.9 100 0.263 14.6 20.4 11312
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 2.8 2.95 100 0.698 4.9 21 1592
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 2.8 47.9 10706 551 99.96 0.20526 0.20211 0.2021 0.26469 0.2615 RANDOM 18.079
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] 0.31 0.16 0.31 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_3_deg 16.723 r_dihedral_angle_4_deg 16.008 r_dihedral_angle_1_deg 6.368 r_mcangle_it 1.537 r_angle_refined_deg 1.356 r_scangle_it 1.069 r_mcbond_it 0.894 r_scbond_it 0.647 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.415 r_dihedral_angle_3_deg 16.723 r_dihedral_angle_4_deg 16.008 r_dihedral_angle_1_deg 6.368 r_mcangle_it 1.537 r_angle_refined_deg 1.356 r_scangle_it 1.069 r_mcbond_it 0.894 r_scbond_it 0.647 r_nbtor_refined 0.308 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.087 r_metal_ion_refined 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_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 2071 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing