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Crystal Structure of D-alanine Carboxypeptidase AmpC from Mycobacterium smegmatis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.2 M Calcium Chloride, 0.1 M Tris:HCl pH 8.5, 25% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.32 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.779 α = 90 b = 73.682 β = 90.19 c = 113.413 γ = 90
Symmetry Space Group C 1 2 1
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 315r 2015-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 97.4 0.092 14.34 3 95577
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 1.8 1.83 96 0.68 1.66 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.8 32.551 1.35 95551 4547 96.72 0.1651 0.1635 0.1633 0.1972 0.197 random
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 14.799 f_angle_d 0.924 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8058 Nucleic Acid Atoms Solvent Atoms 803 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 phasing SBC-Collect data collection