☰ Navigation Tabs
Saccharothrix syringae 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 38% v/v 1,4-Dioxane
Crystal Properties Matthews coefficient Solvent content 2.98 58.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.111 α = 90 b = 97.539 β = 116.72 c = 72.662 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 EIGER2 XE 16M 2022-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 75.18 99.8 0.083 1 15 6.9 90363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 95.9 0.953 0.7 1.1 5.6
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 1.7 75.18 85824 4537 99.79 0.1843 0.18286 0.1931 0.21176 0.2212 RANDOM 34.958
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] -0.09 0.07 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.739 r_long_range_B_refined 6.949 r_long_range_B_other 6.899 r_dihedral_angle_1_deg 6.719 r_scangle_other 4.741 r_scbond_it 3.394 r_scbond_other 3.393 r_mcangle_it 3.306 r_mcangle_other 3.306 r_dihedral_angle_2_deg 2.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.739 r_long_range_B_refined 6.949 r_long_range_B_other 6.899 r_dihedral_angle_1_deg 6.719 r_scangle_other 4.741 r_scbond_it 3.394 r_scbond_other 3.393 r_mcangle_it 3.306 r_mcangle_other 3.306 r_dihedral_angle_2_deg 2.863 r_mcbond_it 2.386 r_mcbond_other 2.386 r_angle_refined_deg 1.622 r_angle_other_deg 0.494 r_chiral_restr 0.14 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4955 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 336
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling PHASER phasing