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crystal structure of the apo form of the N-acetylmuramyl-L-alanine amidase, Ami1, from Mycobacterium abscessus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M Bis-Tris pH 5.5, 1.6 M ammonium sulfate and, 1% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.92 α = 90 b = 85.92 β = 90 c = 73.66 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS PILATUS3 S 6M 2020-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.979 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.6 60.7 99.1 0.09 0.99 10.45 6.3 35745 22.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.65 1.13 0.53
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4LQ6 1.6 38.42 1.35 35743 2000 96.75 0.1698 0.1682 0.1687 0.1959 0.1967 27.64
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.5253 f_angle_d 0.8854 f_chiral_restr 0.0518 f_bond_d 0.0068 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1564 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing