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Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg and dipeptide L-Arg-D-Lys
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 Precipitant contained 25% PEG 3350, 0.1M Tris-HCl, and 0.2M Li2SO4. Protein solution contained 0.1M KCl, 0.05M HEPES (pH 8.0), 0.02M L-Arg-L-Lys, and 0.01M MgCl2. Protein concentration was 12 mg/mL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.45 72.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 275.32 α = 90 b = 275.32 β = 90 c = 275.32 γ = 90
Symmetry Space Group I 21 3
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 RAYONIX MX-300 2010-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 2.7 19.87 99.7 0.154 12.84 21.5 94589 94319 52.4
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 2.7 2.8 100 0.775 2.03 9696
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.701 19.87 1.99 94295 94189 4706 99.97 0.228 0.1775 0.1752 0.1715 0.2215 0.2143 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 17.142 f_angle_d 1.339 f_chiral_restr 0.096 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13600 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 299
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling