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Crystal structure of Efga from Methylobacterium extorquens in complex with formaldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 283.15 0.2 M KNO3, 2.2 M AmSO4, 16.6 mM Formaldehyde
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.059 α = 90 b = 72.063 β = 90 c = 104.555 γ = 90
Symmetry Space Group P 21 2 21
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 MARMOSAIC 300 mm CCD 2013-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97934 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 1.83 50 98.4 0.119 7.4 11.6 48026 20.87
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 1.83 1.86 96.3 0.545 11.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2A2L 1.83 42.315 1.35 47924 1992 98.1 0.2242 0.2224 0.2655 0.2264 26.4895
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 8.941 f_angle_d 0.919 f_chiral_restr 0.057 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3884 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing