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Prenylated-FMN maturase PhdC E45A mutant from Mycolicibacterium fortuitum (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Initial model was wt apo PhdC solved 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 KCl 1mM MnCl2).
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.801 α = 90 b = 75.605 β = 90 c = 80.895 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 2024-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.729 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 1.32 55.24 83.9 0.059 0.063 0.02 0.999 18.8 8.6 36263
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 1.32 1.34 50.7 0.441 0.521 0.269 0.767 2.5 3.4
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 FREE R-VALUE 1.32 48.134 36263 1752 83.54 0.122 0.1204 0.1204 0.1456 0.1456 19.124
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] -2.065 2.447 -0.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.114 r_lrange_it 18.026 r_lrange_other 17.152 r_dihedral_angle_6_deg 15.368 r_scangle_it 14.558 r_scangle_other 14.55 r_dihedral_angle_3_deg 11.318 r_scbond_it 10.461 r_scbond_other 10.455 r_mcangle_other 8.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.114 r_lrange_it 18.026 r_lrange_other 17.152 r_dihedral_angle_6_deg 15.368 r_scangle_it 14.558 r_scangle_other 14.55 r_dihedral_angle_3_deg 11.318 r_scbond_it 10.461 r_scbond_other 10.455 r_mcangle_other 8.542 r_mcangle_it 8.513 r_dihedral_angle_1_deg 6.305 r_mcbond_it 6.19 r_mcbond_other 6.189 r_rigid_bond_restr 5.354 r_angle_refined_deg 2.137 r_angle_other_deg 0.75 r_symmetry_nbd_refined 0.423 r_nbd_other 0.292 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.11 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.065 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling autoPROC data reduction PHASER phasing Coot model building