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X-ray structure of the drug binding domain of AlbA in complex with the KMR-14-14 compound of the pyrrolobenzodiazepines class
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.2M Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 4 69.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.631 α = 90 b = 118.95 β = 92.073 c = 57.702 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 9M 2023-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.17 49.49 99.8 0.055 0.03 0.999 12.3 4.2 64940
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.25 100 1.435 0.764 0.365 0.9 4.4
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 FREE R-VALUE 2.17 49.49 64905 3278 99.745 0.21 0.2084 0.212 0.2337 0.235 68.747
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] 0.489 -0.421 -0.365 -0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 20.761 r_dihedral_angle_3_deg 15.23 r_lrange_other 9.339 r_lrange_it 9.317 r_dihedral_angle_1_deg 4.692 r_scangle_it 3.893 r_scangle_other 3.892 r_mcangle_it 2.863 r_mcangle_other 2.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.335 r_dihedral_angle_4_deg 20.761 r_dihedral_angle_3_deg 15.23 r_lrange_other 9.339 r_lrange_it 9.317 r_dihedral_angle_1_deg 4.692 r_scangle_it 3.893 r_scangle_other 3.892 r_mcangle_it 2.863 r_mcangle_other 2.862 r_scbond_it 2.309 r_scbond_other 2.309 r_mcbond_it 1.722 r_mcbond_other 1.722 r_angle_refined_deg 1.273 r_angle_other_deg 1.187 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.209 r_symmetry_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.173 r_nbd_other 0.173 r_nbtor_refined 0.158 r_ncsr_local_group_1 0.096 r_ncsr_local_group_3 0.09 r_ncsr_local_group_2 0.085 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.055 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.012 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5358 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 370
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing