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Structure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.6 M sodium/potassium phosphate, 100 mM Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.133 α = 90 b = 93.061 β = 90 c = 94.094 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 210r 2015-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.4 66.2 99.58 0.054 0.998 12.4 3 30442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 68.3 0.32 0.908 3.6 3
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 5TZD 2.4 66.166 1.98 30442 1485 99.58 0.2315 0.2294 0.2278 0.2719 0.2685 58.59
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] 1.2017 1.4629 -2.6646
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 39.37 f_angle_d 1.096 f_chiral_restr 0.408 f_bond_d 0.011 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4822 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 368
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction