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Crystal Structure of RT-PhyR (ruthe_01174)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 0.1M Tris.HCl pH 8.5, 16% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.24 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.91 α = 90 b = 118.642 β = 90 c = 121.088 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS EIGER X 16M Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2024-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 1.99 34 100 0.108 0.112 0.03 0.999 13.4 13.7 56844 43.03
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 1.99 2.02 100 3.462 3.59 0.944 0.352 0.8 14.2
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 1.99 34 1.34 56818 2675 99.95 0.2101 0.2087 0.2072 0.2373 0.2349 54.23
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 16.5612 f_angle_d 1.3441 f_chiral_restr 0.0656 f_plane_restr 0.0473 f_bond_d 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5752 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data processing Aimless data scaling PHASER phasing Coot model building BALBES phasing ARP/wARP model building