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Crystal structure of arylmalonate decarboxylase (AMDase) from Bordatella bronchiseptic in complex with benzylphosphonate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 well solution 0.1M Tris pH 8.0 and 30% Peg 10K, Protein 10-15mg/ml in Tris pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.93 36.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.64 α = 90 b = 65.6 β = 110.42 c = 41.88 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 ADSC QUANTUM 315 Monochromator 2008-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9756 Diamond I02
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 1.498 50 0.061 12.6 63157 29865 1
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS 1.498 32.955 1.99 29863 1511 94.83 0.1594 0.1582 0.1567 0.1806 0.1759 16.151
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] -2.991 -1.61 -4.294 2.556
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.551 f_angle_d 1.351 f_chiral_restr 0.085 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1671 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 11
Software Software Software Name Purpose DNA data collection PHENIX model building PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing