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Structure of a bacteria protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 291.15 Polyethylene glycol 3350, Tris, Cobalt(II) chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.775 α = 85.6 b = 75.745 β = 89.16 c = 119.706 γ = 89.37
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 PILATUS3 6M 2021-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 48.67 90.99 0.998 9.78 3.6 52101 24.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 0.968
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Alphafold2 2.3 48.67 1.97 52010 2588 91 0.1883 0.1863 0.1865 0.2275 0.2274 34.07
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 5.0599 f_angle_d 0.6407 f_chiral_restr 0.043 f_plane_restr 0.0074 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10737 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction autoPROC data scaling PHENIX phasing