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Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to prenylated flavin mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PhdC apo model 1.5A structure solved previously from our group
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 1:1 crystallization condition (100 mM Citric acid/NaOH pH 5, 20% (w/v) PEG 6K) to protein (20mM bistris pH 7.2, 200mM KCl, reconstituted with prFMN)
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.192 α = 90 b = 75.07 β = 90 c = 80.264 γ = 90
Symmetry Space Group I 2 2 2
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 CdTe 16M 2024-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
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 1.81 30.51 99.9 0.08 0.086 0.025 0.999 14.4 10.9 16947
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 1.81 1.85 98.7 0.741 0.804 0.3 0.846 2.3 6.4
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 THROUGHOUT 1.81 29.604 16946 871 99.829 0.158 0.1561 0.1681 0.1866 0.2018 40.362
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] 0.163 -0.511 0.348
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 37.941 r_scbond_other 37.931 r_scangle_it 31.999 r_scangle_other 31.982 r_dihedral_angle_other_1_deg 27.278 r_lrange_it 23.998 r_lrange_other 23.998 r_dihedral_angle_6_deg 15.401 r_dihedral_angle_3_deg 13.175 r_mcangle_other 10.129
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 37.941 r_scbond_other 37.931 r_scangle_it 31.999 r_scangle_other 31.982 r_dihedral_angle_other_1_deg 27.278 r_lrange_it 23.998 r_lrange_other 23.998 r_dihedral_angle_6_deg 15.401 r_dihedral_angle_3_deg 13.175 r_mcangle_other 10.129 r_mcangle_it 10.094 r_mcbond_other 9.913 r_mcbond_it 9.877 r_dihedral_angle_2_deg 8.948 r_dihedral_angle_1_deg 7.255 r_angle_refined_deg 1.833 r_angle_other_deg 0.764 r_nbd_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.168 r_symmetry_nbd_other 0.164 r_xyhbond_nbd_refined 0.145 r_metal_ion_refined 0.132 r_symmetry_nbd_refined 0.13 r_nbd_other 0.121 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.081 r_xyhbond_nbd_other 0.027 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building