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Photosensory module from DrBphP without PHY tongue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 12% polyethylene glycol (PEG) 3350, 200 mM ammonium acetate, 5% fructose, 5% glucose, and 100 mM sodium citrate pH5.6
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.63 α = 90 b = 64.59 β = 91.55 c = 131.04 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F Toroidal mirror 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.07225 ESRF ID23-1
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 2.3 50 98.8 0.152 0.181 0.989 5.4 3.292 88343
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.2 1.496 1.792 0.325 3.259
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K5B 2.3 45.99 83924 4418 98.82 0.23667 0.235 0.26819 0.2627 RANDOM 50.392
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] 2.18 0.52 -0.02 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.018 r_long_range_B_refined 7.553 r_long_range_B_other 7.55 r_dihedral_angle_1_deg 6.289 r_dihedral_angle_2_deg 5.137 r_scangle_other 4.58 r_mcangle_it 4.401 r_mcangle_other 4.401 r_scbond_it 2.815 r_scbond_other 2.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.018 r_long_range_B_refined 7.553 r_long_range_B_other 7.55 r_dihedral_angle_1_deg 6.289 r_dihedral_angle_2_deg 5.137 r_scangle_other 4.58 r_mcangle_it 4.401 r_mcangle_other 4.401 r_scbond_it 2.815 r_scbond_other 2.815 r_mcbond_it 2.716 r_mcbond_other 2.714 r_angle_refined_deg 0.989 r_angle_other_deg 0.362 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14041 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction