☰ Navigation Tabs
Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to prenylated flavin mononucleotide in the P1 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Apo PhdC solved previously by our group, deposited as 9NK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 1:2 condition (100 mM citric acid/NaOH pH 5.0, 20% w/v PEG 6K) to buffer (20 mM BisTris pH 7.2 200 mM KCl). Protein reconstituted with prFMN
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.552 α = 69.95 b = 60.19 β = 85.032 c = 65.053 γ = 65.414
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 PILATUS 6M 2024-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.976 SSRL BL9-2
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 1.62 51.5 85.4 0.04 0.047 0.024 0.999 18.8 3.8 75219
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 1.62 1.65 50.5 0.181 0.21 0.106 0.97 5.9 3.9
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 FREE R-VALUE 1.62 51.499 75118 3712 85.323 0.169 0.168 0.168 0.1955 0.1955 21.655
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] 0.4 -0.078 0.614 -0.233 0.159 -0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.088 r_dihedral_angle_3_deg 12.51 r_dihedral_angle_2_deg 9.909 r_lrange_it 7.258 r_dihedral_angle_1_deg 6.658 r_scangle_it 5.884 r_scbond_it 3.961 r_mcangle_it 2.97 r_angle_refined_deg 2.15 r_mcbond_it 2.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.088 r_dihedral_angle_3_deg 12.51 r_dihedral_angle_2_deg 9.909 r_lrange_it 7.258 r_dihedral_angle_1_deg 6.658 r_scangle_it 5.884 r_scbond_it 3.961 r_mcangle_it 2.97 r_angle_refined_deg 2.15 r_mcbond_it 2.082 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.176 r_chiral_restr 0.143 r_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.098 r_ncsr_local_group_1 0.085 r_ncsr_local_group_5 0.083 r_ncsr_local_group_4 0.077 r_ncsr_local_group_2 0.068 r_ncsr_local_group_6 0.068 r_ncsr_local_group_3 0.064 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4791 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building