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Structure of YhdA, K109D/D137K variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NNI PDB entry 1nni
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch crystallization 8.5 298 0.1 M Tris pH 8.5, 2.0 M Ammonium Sulfate, batch crystallization, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.625 α = 90 b = 170.132 β = 92.25 c = 93.289 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 IMAGE PLATE MAR scanner 345 mm plate 2005-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8148 EMBL/DESY, HAMBURG X13
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 2.105 30 96.7 0.096 3.6 119393 119393 31.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.105 2.16 52.5 0.46 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 1nni 2.105 29.341 119393 119393 6012 96.7 0.187 0.187 0.185 0.221 0.2048 RANDOM 36.237
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] 7.422 0.498 -4.633 -2.789
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.06 f_angle_d 0.58 f_chiral_restr 0.039 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15379 Nucleic Acid Atoms Solvent Atoms 977 Heterogen Atoms 372
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection DENZO data reduction SCALEPACK data scaling PHASER phasing