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Crystal structure of the flavoprotein monooxygenase GrhO5 from griseorhodin A biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 20 % PEG 3350, 200 mM di-Sodium malonate
Crystal Properties Matthews coefficient Solvent content 1.96 37.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.069 α = 90 b = 104.437 β = 104.886 c = 69.226 γ = 90
Symmetry Space Group P 1 21 1
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 2020-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 44.563 97.8 0.15 0.09 0.98 5 3.2 62285
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 0.63 0.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3IHG 1.75 44.52 61964 3117 97.23 0.196 0.1943 0.2018 0.2327 0.2375 23.034
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] 0.029 0.002 -0.042 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.142 r_dihedral_angle_4_deg 18.905 r_dihedral_angle_3_deg 13.009 r_dihedral_angle_1_deg 6.706 r_lrange_it 6.036 r_lrange_other 5.845 r_scangle_it 4.412 r_scangle_other 4.411 r_mcangle_it 2.916 r_mcangle_other 2.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.142 r_dihedral_angle_4_deg 18.905 r_dihedral_angle_3_deg 13.009 r_dihedral_angle_1_deg 6.706 r_lrange_it 6.036 r_lrange_other 5.845 r_scangle_it 4.412 r_scangle_other 4.411 r_mcangle_it 2.916 r_mcangle_other 2.915 r_scbond_other 2.828 r_scbond_it 2.826 r_mcbond_it 1.965 r_mcbond_other 1.958 r_angle_refined_deg 1.594 r_angle_other_deg 1.445 r_nbd_refined 0.202 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.163 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.084 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3885 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing