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Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium fortuitum bound to flavin mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Apo wt PhdC model solved previously by our group (deposition in progress)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1:1 crystallization condition (0.2M ammonium acetate, 0.1M HEPES/NaOH pH 7.5, 45% v/v MPD) to buffer (20 mM BisTris pH 7.2 200 mM)
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.003 α = 90 b = 76.007 β = 90 c = 80.115 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 2024-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.689 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 1.27 30.52 98.3 0.082 0.086 0.026 0.998 15 10.3 47805
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 1.27 1.29 84.7 0.828 0.94 0.423 0.516 2.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.27 30.512 47802 1829 98.332 0.129 0.1285 0.1308 0.1492 0.1507 19.346
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] -1.138 0.378 0.76
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.576 r_lrange_other 16.774 r_dihedral_angle_6_deg 15.599 r_dihedral_angle_2_deg 11.953 r_dihedral_angle_3_deg 11.747 r_scangle_it 11.348 r_scangle_other 11.342 r_scbond_other 8.406 r_scbond_it 8.391 r_mcangle_other 7.062
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.576 r_lrange_other 16.774 r_dihedral_angle_6_deg 15.599 r_dihedral_angle_2_deg 11.953 r_dihedral_angle_3_deg 11.747 r_scangle_it 11.348 r_scangle_other 11.342 r_scbond_other 8.406 r_scbond_it 8.391 r_mcangle_other 7.062 r_mcangle_it 7.052 r_dihedral_angle_1_deg 6.723 r_mcbond_it 5.229 r_mcbond_other 5.226 r_rigid_bond_restr 4.49 r_angle_refined_deg 1.972 r_angle_other_deg 0.888 r_xyhbond_nbd_other 0.351 r_symmetry_nbd_refined 0.267 r_nbd_refined 0.258 r_symmetry_xyhbond_nbd_refined 0.244 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.174 r_nbd_other 0.168 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.013 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 1179 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing Coot model building