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Crystal structure of Bacillus subtilus YdiB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 42 % PEG600 and 200 mM Imidazole malate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.59 α = 90 b = 59.82 β = 110.09 c = 39.34 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2016-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07252 ESRF ID29
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 1.76 43.84 98.6 0.032 16.5 3.2 14655 31.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1HTW 1.762 43.835 1.39 14651 708 98.57 0.1816 0.1802 0.1824 0.2091 0.2128
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 19.29 f_angle_d 1.227 f_chiral_restr 0.062 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1161 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing