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Crystal structure of PpSB1-LOV protein from Pseudomonas putida in covalent complex with 5-deazaflavin mononucleotide (5dFMN)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% PEG3350, 0.2 M Ammonium formate, 0.1 M bis-tris propane pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.245 α = 90 b = 61.852 β = 90 c = 107.106 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 2M 2025-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 1.57 53.6 94.9 0.994 6.5 2.4 46117
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 1.57 1.59 0.399 0.9
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 1.57 53.56 43731 2281 94.65 0.18707 0.18561 0.1971 0.21362 0.2185 RANDOM 26.758
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] 2.5 -1.32 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.797 r_dihedral_angle_2_deg 7.098 r_long_range_B_refined 6.882 r_long_range_B_other 6.88 r_dihedral_angle_1_deg 6.012 r_scangle_other 5.35 r_mcangle_it 3.592 r_mcangle_other 3.592 r_scbond_it 3.488 r_scbond_other 3.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.797 r_dihedral_angle_2_deg 7.098 r_long_range_B_refined 6.882 r_long_range_B_other 6.88 r_dihedral_angle_1_deg 6.012 r_scangle_other 5.35 r_mcangle_it 3.592 r_mcangle_other 3.592 r_scbond_it 3.488 r_scbond_other 3.486 r_mcbond_it 2.406 r_mcbond_other 2.405 r_angle_refined_deg 1.603 r_angle_other_deg 0.568 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2172 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction