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Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 2:1 protein (20mM bistris pH 7.2, 200mM KCl, 1mM MnCl2, 5% glycerol) 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 2.48 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.083 α = 90 b = 76.697 β = 90 c = 80.594 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) 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 1.52 38.35 99.7 0.025 0.027 1 46 6.6 28916
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 1.52 1.55 99.8 0.98 0.106 0.57 0.995 16.9 6.7
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 1.52 38.348 28916 1502 99.539 0.129 0.1267 0.1279 0.1648 0.1659 19.046
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] -2.107 0.22 1.887
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.394 r_lrange_other 15.906 r_dihedral_angle_6_deg 14.662 r_dihedral_angle_2_deg 14.155 r_dihedral_angle_3_deg 11.838 r_scangle_it 11.826 r_scangle_other 11.82 r_scbond_it 8.396 r_scbond_other 8.392 r_mcangle_other 7.887
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.394 r_lrange_other 15.906 r_dihedral_angle_6_deg 14.662 r_dihedral_angle_2_deg 14.155 r_dihedral_angle_3_deg 11.838 r_scangle_it 11.826 r_scangle_other 11.82 r_scbond_it 8.396 r_scbond_other 8.392 r_mcangle_other 7.887 r_mcangle_it 7.88 r_dihedral_angle_1_deg 6.911 r_mcbond_it 5.513 r_mcbond_other 5.513 r_rigid_bond_restr 5.272 r_angle_refined_deg 1.977 r_angle_other_deg 0.805 r_nbd_refined 0.247 r_symmetry_xyhbond_nbd_refined 0.213 r_symmetry_nbd_refined 0.189 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.166 r_symmetry_nbd_other 0.163 r_nbd_other 0.123 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.077 r_metal_ion_refined 0.073 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1198 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing