☰ Navigation Tabs
Acidimicrobiaceae bacterium photocobilins protein, dark state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 8% PEG 20,000, 8% PEG 550 MME, 0.1M Sodium acetate pH5.5, 0.2M Potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.85 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.773 α = 90 b = 125.836 β = 90 c = 124.63 γ = 90
Symmetry Space Group C 2 2 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 XE 16M 2021-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 44.31 99.86 0.1766 6.95 13.7 38287
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 99.79 0.9439 0.94 13.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 44.31 36286 1996 99.97 0.21085 0.20935 0.2125 0.23664 0.242 RANDOM 63.721
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] 0.19 -2.59 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.656 r_dihedral_angle_1_deg 7.819 r_long_range_B_other 6.269 r_long_range_B_refined 6.267 r_scangle_other 2.708 r_mcangle_it 2.685 r_mcangle_other 2.685 r_angle_refined_deg 1.768 r_scbond_it 1.711 r_scbond_other 1.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.656 r_dihedral_angle_1_deg 7.819 r_long_range_B_other 6.269 r_long_range_B_refined 6.267 r_scangle_other 2.708 r_mcangle_it 2.685 r_mcangle_other 2.685 r_angle_refined_deg 1.768 r_scbond_it 1.711 r_scbond_other 1.691 r_mcbond_it 1.636 r_mcbond_other 1.624 r_angle_other_deg 0.535 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4874 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling PHASER phasing