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Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to flavin mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously acquired apo PhdC solution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1:2 protein (20mM bistris pH 7.2, 200mM KCl, 1mM MnCl2, 5% glycerol +FMN reconstitution) to condition (30% w/v PEG 5000 MME, 100 mM MES/ Sodium hydroxide pH 6.5, 200 mM ammonium sulfate)
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.039 α = 90 b = 75.032 β = 90 c = 79.746 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 EIGER X 16M 2024-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.987 SSRL BL12-1
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 1.23 47.97 84.2 0.035 0.038 0.015 0.999 18.3 5.6 44741
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 1.23 1.25 32.2 0.559 0.733 0.466 0.508 1.3 2.3
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 1.23 47.965 44079 2174 83.882 0.132 0.1308 0.1308 0.1481 0.1492 19.907
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] -2.302 4.46 -2.158
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.302 r_lrange_other 16.206 r_dihedral_angle_2_deg 15.901 r_dihedral_angle_6_deg 14.849 r_scangle_it 12.855 r_scangle_other 12.594 r_dihedral_angle_3_deg 10.076 r_scbond_it 9.15 r_scbond_other 8.922 r_mcangle_other 7.843
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.302 r_lrange_other 16.206 r_dihedral_angle_2_deg 15.901 r_dihedral_angle_6_deg 14.849 r_scangle_it 12.855 r_scangle_other 12.594 r_dihedral_angle_3_deg 10.076 r_scbond_it 9.15 r_scbond_other 8.922 r_mcangle_other 7.843 r_mcangle_it 7.804 r_rigid_bond_restr 6.89 r_dihedral_angle_1_deg 6.645 r_mcbond_it 5.87 r_mcbond_other 5.791 r_angle_refined_deg 2.14 r_angle_other_deg 0.77 r_nbd_refined 0.228 r_symmetry_nbd_other 0.199 r_symmetry_nbd_refined 0.199 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.187 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_other 0.13 r_chiral_restr 0.124 r_symmetry_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.068 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1182 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing Blu-Ice data collection Coot model building