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Saccharothrix syringae photocobilins protein, light 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 0.2M Potassium citrate tribasic monohydrate 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.68 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.667 α = 90 b = 109.667 β = 90 c = 98.074 γ = 120
Symmetry Space Group P 32 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 2022-07-08 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) 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 1.98 98.07 99.92 0.07186 0.074 1 20.64 20.6 47811
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 100 2.404 0.6 0.67
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 1.98 94.97 45541 2271 100 0.18394 0.18316 0.1936 0.20029 0.2055 RANDOM 60.837
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] -0.21 -0.11 -0.21 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.364 r_long_range_B_refined 7.542 r_long_range_B_other 7.537 r_dihedral_angle_1_deg 6.039 r_scangle_other 4.758 r_mcangle_it 3.624 r_mcangle_other 3.623 r_scbond_it 3.156 r_scbond_other 3.155 r_mcbond_it 2.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.364 r_long_range_B_refined 7.542 r_long_range_B_other 7.537 r_dihedral_angle_1_deg 6.039 r_scangle_other 4.758 r_mcangle_it 3.624 r_mcangle_other 3.623 r_scbond_it 3.156 r_scbond_other 3.155 r_mcbond_it 2.405 r_mcbond_other 2.405 r_dihedral_angle_2_deg 1.745 r_angle_refined_deg 1.551 r_angle_other_deg 0.481 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement DIALS data reduction XSCALE data scaling PHASER phasing