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X-ray crystal structure of the Pyr1-pyrabactin A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JRS PDB entry 3JRS, subunit A only
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Protein solution 100 nl- 20 mM NaCl, 2 mM DTT 20 mM Tris, pH 7.6, Precipitant solution 100 nl- 2.0 M ammonium sulfate, 100 mM BisTris, pH 5.5, Cryoprotectant- Fomblin 06/6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.307 α = 90 b = 60.307 β = 90 c = 527.599 γ = 120
Symmetry Space Group P 61 2 2
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 MARMOSAIC 300 mm CCD 2009-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0781 APS 21-ID-D
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 2.47 50 95.3 0.086 10.3 5.4 21108
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.47 2.51 93.1 0.509 4.4 1018
Refinement Statistics Diffraction ID Structure Solution 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 3JRS, subunit A only 2.473 32.046 0.1 19707 1882 89.75 0.226 0.2218 0.22 0.2654 0.2626 random 54.958
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] 5.6398 5.6398 -11.2797
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.951 f_angle_d 1.572 f_chiral_restr 0.13 f_bond_d 0.026 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4156 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 77
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing