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Crystal structure of Arr-2 in complex with Rifampicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 5 mg/ml, 1 mM inhibitor (7-chloro-2-{4-[(2-hydroxyethyl)(methyl)amino]phenyl}-3,4-dihydroquinazolin-4-one), 1 mM rifampicin, 100 mM MOPS pH 7.5, 20% ethanol, and 2.7 M (NH4)2 SO4.
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.26 α = 90 b = 42.97 β = 90 c = 85.49 γ = 90
Symmetry Space Group P 21 21 21
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 2024-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 1.4 50 99.6 0.998 12.41 5.01 30653
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 1.4 1.44 99.8 0.784 2.12 5.12
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.4 38.423 30602 1531 99.639 0.145 0.1431 0.143 0.1846 0.1842 22.01
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] -0.266 -0.193 0.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.931 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_4_deg 10.798 r_dihedral_angle_1_deg 7.059 r_lrange_it 5.717 r_lrange_other 5.59 r_scangle_other 5.113 r_scangle_it 5.109 r_scbond_it 4.349 r_scbond_other 4.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.931 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_4_deg 10.798 r_dihedral_angle_1_deg 7.059 r_lrange_it 5.717 r_lrange_other 5.59 r_scangle_other 5.113 r_scangle_it 5.109 r_scbond_it 4.349 r_scbond_other 4.339 r_mcangle_other 3.513 r_mcangle_it 3.502 r_mcbond_it 2.78 r_rigid_bond_restr 2.706 r_mcbond_other 2.658 r_angle_refined_deg 1.662 r_angle_other_deg 1.367 r_symmetry_nbd_refined 0.225 r_nbd_other 0.215 r_nbd_refined 0.21 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.124 r_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.081 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1155 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing