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Crystal structure of copper-loaded SmAA10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 precipitant: 0.1 M citric acid (pH 3.7), 25% w/v PEG 3350; protein solution: holo-SmAA10 (15 mg/mL) in 50 mM MES (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.08 40.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.646 α = 90 b = 106.738 β = 99.955 c = 55.459 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 PILATUS 6M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.9795 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.4556 27.312 98.4 0.0898 0.1064 0.996 9.01 3.5 52821 14.9368265296
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.456 1.508 96 0.9846 1.176 0.567 1.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.4556132868 27.3119999955 1.3506060771 52798 1998 98.4174324753 0.161523858793 0.160459392301 0.161 0.188484156567 0.1881 19.0581766013
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 16.5675771228 f_angle_d 0.760278042579 f_chiral_restr 0.0785824620844 f_plane_restr 0.00540405792037 f_bond_d 0.00372837053406
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2650 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing