☰ Navigation Tabs
A.fulgidus RioK1 bound to small molecule KPSH02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.06 M divalent cations (MgCl2/CaCl2), 0.1 M Buffer system 1 (Imidazole and MES monohydrate), pH 6.5, and 30% (v/v) Precipitant mix 1 (40% v/v PEG 500 MME, 20% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.339 α = 90 b = 75.24 β = 90.23 c = 60.949 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2022-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920092 NSLS-II 17-ID-1
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 1.76 60.9 93.1 0.155 0.196 0.119 0.988 5.7 4.9 29191 18.86
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 1.76 1.935 57.3 0.982 1.199 0.682 0.576 1.5
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 1.76 40.06 1.38 29178 1413 61.52 0.2095 0.2068 0.207 0.2608 0.2616 26.42
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 6.5026 f_angle_d 1.3402 f_chiral_restr 0.0625 f_bond_d 0.0143 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3692 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 52
Software Software Software Name Purpose HKL-3000 data collection PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing