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Room temperature neutron/X-ray structure of sisomicin bound AAC-VIa
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 285 0.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 15-17% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.59 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.822 α = 90 b = 86.169 β = 94.55 c = 76.9 γ = 90
Symmetry Space Group I 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 298 IMAGE PLATE RIGAKU RAXIS IV++ 2017-07-01 M SINGLE WAVELENGTH 2 1 neutron 298 DIFFRACTOMETER ORNL ANGER CAMERA 2017-07-01 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 2 NUCLEAR REACTOR ORNL Spallation Neutron Source BEAMLINE MANDI 2.0-4.0 ORNL Spallation Neutron Source MANDI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.9 50 99.25 0.047 0.067 0.047 0.997 17.2 1.66 25874 32.2 2 2.2 15.57 92.2 0.148 0.173 0.087 0.979 10.2 3.4 15860 32.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 0.401 0.511 0.313 0.839 2.1 1 1.97 2.05 0.321 0.406 0.246 0.886 2.4 1 2.05 2.14 0.243 0.307 0.185 0.926 2.4 1 2.14 2.25 0.165 0.208 0.125 0.963 2.4 1 2.25 2.39 0.127 0.161 0.097 0.978 2.4 1 2.39 2.58 0.089 0.112 0.067 0.989 2.4 1 2.58 2.84 0.065 0.081 0.049 0.992 2.4 1 2.84 3.25 0.045 0.056 0.033 0.996 2.4 1 3.25 4.09 0.031 0.038 0.023 0.998 2.5 1 4.09 50 0.031 0.038 0.023 0.997 2.4
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.9 38.329 1.34 25867 1286 99.23 0.1519 0.1503 0.1529 0.1814 0.1854 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.2 15.433 15512 763 92.47 0.1987 0.1976 0.2199
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 19.476 f_dihedral_angle_d 19.476 f_angle_d 0.81 f_angle_d 0.81 f_chiral_restr 0.074 f_chiral_restr 0.074 f_bond_d 0.013 f_bond_d 0.013 f_plane_restr 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2023 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing