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Neutron/X-ray crystal structure of AAC-VIa bound to gentamicin C1A
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 polyethylene glycol (PEG) 8000, 0.2 M MgCl2, 0.1 M Tris, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.319 α = 90 b = 86.228 β = 120.4 c = 51.003 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 293 IMAGE PLATE RIGAKU RAXIS IV++ 2018-01-01 M SINGLE WAVELENGTH 2 1 neutron 293 AREA DETECTOR ORNL ANGER CAMERA 2018-01-01 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 98.4 0.056 0.068 0.039 18.8 2.8 26002 34.34 2 2.35 16.8 76.9 0.117 0.146 0.085 0.989 8 2.6 10677 34.34
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 0.658 0.822 0.484 0.671 2.6 1 1.97 2.05 0.518 0.646 0.379 0.726 2.8 1 2.05 2.14 0.36 0.447 0.26 0.85 2.8 1 2.14 2.25 0.26 0.322 0.186 0.906 2.8 1 2.25 2.39 0.176 0.217 0.126 0.951 2.8 1 2.39 2.58 0.127 0.157 0.091 0.977 2.8 1 2.58 2.84 0.083 0.103 0.059 0.988 2.8 1 2.84 3.25 0.052 0.064 0.037 0.995 2.9 1 3.25 4.09 0.035 0.043 0.024 0.997 2.9 1 4.09 50 0.037 0.045 0.025 0.996 3 2 2.35 2.48 0.29 0.204 2.5
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 43.114 1.34 25996 1304 98.27 0.1588 0.1566 0.1997 54.987 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.35 16.8 10675 535 76.08 0.2671 0.2648 0.3092
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-3000 data scaling PHASER phasing