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Crystal structure of RamR with Tyr59 replaced with para-boronophenylalanine (boronate form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein solution: 13 mg/ml in 20 mM Hepes, pH 8, 500 mM NaCl. Reservoir solution: 0.1 M Tris, pH 8.5, 20% ethanol. Drops of 200 nL were prepared by mixing protein solution and reservoir solution (1:1)
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.872 α = 90 b = 51.88 β = 96.49 c = 118.319 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 PILATUS 6M 2024-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965460 ESRF MASSIF-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 2.78 78 93.4 0.075 0.091 0.051 0.996 8.5 2.9 22672
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 2.78 2.93 64.3 0.457 0.61 0.399 0.684 1.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.78 78 1.37 22661 1186 93.32 0.2129 0.2105 0.2167 0.2568 0.2644 RANDOM
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 15.562 f_angle_d 1.215 f_chiral_restr 0.052 f_plane_restr 0.012 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5934 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement