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RamR variant D2.3 complexed with 1-phenyl-dihydroisoquinoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1M NaCl, 0.2M Ammonium Sulfate, 0.1M MES pH 6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.107 α = 90 b = 57.107 β = 90 c = 449.903 γ = 120
Symmetry Space Group P 65 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 PILATUS3 6M 2023-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 2.37 449.9 100 0.336 0.345 0.077 0.976 7.8 20 19261
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 2.37 2.41 99.7 3.174 3.253 0.705 0.424 21
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 2.37 49.46 1.33 19096 1910 99.92 0.2728 0.2671 0.2713 0.3261 0.3288
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 13.86 f_angle_d 1.008 f_chiral_restr 0.052 f_plane_restr 0.009 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2876 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement xia2 data scaling xia2 data reduction PHENIX phasing