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Pseudomonas putida KT2440 IclR-type transcription factor (PP_2609)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M Tris-HCl pH 8,
0.2M Li2SO4,
0.02M Ammonium Acetate,
8% w/v PEG3350,
Arabidopsis thaliana root exudates
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.598 α = 90 b = 69.44 β = 101.99 c = 95.684 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 80 PIXEL DECTRIS PILATUS 6M 2014-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 93.5 99.58 0.11 0.132 0.071 0.986 7.2 3.4 66102 32.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.108 2.115 99.6 0.461 0.554 0.305 0.778 2.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 MOLECULAR REPLACEMENT FREE R-VALUE 2.11 38.09 1.34 66079 3276 99.6 0.1982 0.1955 0.1955 0.2521 0.2494 37.49
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 5.9542 f_angle_d 0.9106 f_chiral_restr 0.0531 f_plane_restr 0.0101 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7854 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHENIX phasing