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Crystal structure of Arr in complex with Rifampicin and Chr-16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 293 10 mg/ml protein, 1 mM rifampicin, 1 mM inhibitor (Chr-16), 50 mM Tris pH 8.2, 0.2 M MgCl2, 10% (w/v) PEG 8000, 20% (v/v) 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.22 α = 90 b = 60.76 β = 93.485 c = 45.55 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 X 16M 2023-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953745 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 45.466 99.4 0.999 12.53 10.99 7819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 96.4 0.797 1.87 6.69
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.2 45.466 7819 506 99.428 0.191 0.187 0.1989 0.2503 0.2154 Random selection 46.161
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] 2.807 -0.046 -2.545 -0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.358 r_dihedral_angle_3_deg 16.949 r_dihedral_angle_4_deg 16.733 r_lrange_it 10.665 r_lrange_other 10.661 r_scangle_it 8.077 r_scangle_other 8.073 r_mcangle_it 6.949 r_mcangle_other 6.945 r_dihedral_angle_1_deg 6.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.358 r_dihedral_angle_3_deg 16.949 r_dihedral_angle_4_deg 16.733 r_lrange_it 10.665 r_lrange_other 10.661 r_scangle_it 8.077 r_scangle_other 8.073 r_mcangle_it 6.949 r_mcangle_other 6.945 r_dihedral_angle_1_deg 6.939 r_scbond_it 5.91 r_scbond_other 5.905 r_mcbond_it 4.981 r_mcbond_other 4.978 r_angle_refined_deg 1.865 r_angle_other_deg 1.335 r_nbd_other 0.249 r_nbd_refined 0.202 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.134 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1099 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing