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Crystal structure of PpSB1-LOV protein from Pseudomonas putida with covalent FMN
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 7 294 15% PEG3350, 10 mM MgCl 2 , 5 mM NiCl 2 and 100 mM
HEPES buffer pH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.926 α = 90 b = 153.926 β = 90 c = 36.039 γ = 120
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 2022-11-03 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) R Merge I (Observed) Rrim I (All) Rpim 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 2.4 44.43 94.7 0.058 0.078 0.052 0.968 11.8 1.9 11764
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 97 0.458 0.604 0.39 0.722 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 38.511 11679 602 93.973 0.23 0.227 0.231 0.2944 0.2902 73.384
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] -0.151 -0.075 -0.151 0.489
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.147 r_lrange_other 17.147 r_dihedral_angle_3_deg 16.784 r_dihedral_angle_6_deg 15.944 r_scangle_it 13.644 r_scangle_other 13.64 r_dihedral_angle_2_deg 12.017 r_mcangle_it 11.838 r_mcangle_other 11.834 r_scbond_it 9.778
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.147 r_lrange_other 17.147 r_dihedral_angle_3_deg 16.784 r_dihedral_angle_6_deg 15.944 r_scangle_it 13.644 r_scangle_other 13.64 r_dihedral_angle_2_deg 12.017 r_mcangle_it 11.838 r_mcangle_other 11.834 r_scbond_it 9.778 r_scbond_other 9.755 r_mcbond_it 8.696 r_mcbond_other 8.696 r_dihedral_angle_1_deg 7.475 r_angle_refined_deg 1.671 r_symmetry_xyhbond_nbd_refined 0.6 r_angle_other_deg 0.564 r_symmetry_nbd_refined 0.407 r_xyhbond_nbd_other 0.402 r_nbd_other 0.375 r_nbd_refined 0.23 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.194 r_ncsr_local_group_1 0.166 r_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2156 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing