☰ Navigation Tabs
Crystal Structure of the Listeria monocytogenes CadC with Cadmium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9T6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Hepes pH7.5, 10 % 2-Propanol, 20 % PEG 4K, 15 % glycerol
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.004 α = 90 b = 64.574 β = 90 c = 102.705 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 EIGER2 X 9M 2024-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8856 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 40.19 98.87 0.1043 0.1266 0.07059 0.998 5.81 3 54092 34.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 98.17 1.727 2.115 1.196 0.373 0.64 2.9
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 FREE R-VALUE 2 40.19 1.33 53783 2669 97.91 0.2063 0.2043 0.2062 0.2415 0.2472 44.86
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 11.8241 f_angle_d 0.4146 f_chiral_restr 0.0353 f_plane_restr 0.002 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3473 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing