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BrxR, a WYL-domain containing transcriptional regulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold BrxR AF2 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 BTP pH 7.5 0.1M
Sodium Sulphate 0.2M
PEG 3350 20%
1:1 ratio
Final BrxR conc @ 5 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.125 α = 90 b = 131.125 β = 90 c = 358.359 γ = 90
Symmetry Space Group P 41 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 EIGER2 X 16M 2021-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.15 82.35 100 0.04 0.057 0.998 9.5 1.9 169928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 100 0.625 0.884 0.567 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE BrxR AF2 model 2.15 82.35 1.35 169717 8437 99.95 0.2209 0.2197 0.2443 0.2156 59.75
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 12.5481 f_angle_d 1.1603 f_chiral_restr 0.071 f_plane_restr 0.0085 f_bond_d 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18437 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing