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Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 Precipitant contained 10% PEG 4000, 0.2M MgSO4 and 0.1M MES. Protein solution contained 0.1M KCl, 0.05M HEPES (pH 8.0), 0.005M L-Arg-L-Lys, and 0.005M MgCl2. Protein concentration was 10 mg/mL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.61 52.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.19 α = 90 b = 150.67 β = 104.66 c = 106.02 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-300 2010-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9792 APS 21-ID-D
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 2.2 19.9 99.8 0.113 13.03 121739 121455 -3 33.315
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 2.2 2.24 100 0.608 3.45
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2.2 19.895 2 121430 121424 6073 99.96 0.207 0.1771 0.1744 0.2289 0.2053 random 29.0025
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] -0.3527 -0.5126 0.7574 -0.4047
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.708 f_angle_d 1.264 f_chiral_restr 0.095 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15827 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 83
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction