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Crystal structure of the flavoprotein monooxygenase RubL from rubromycin 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 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA pH 7.5 buffer system, 12.5% PEG 4000 and 20% 1,2,6-Hexanetriol
Crystal Properties Matthews coefficient Solvent content 2.34 47.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.323 α = 90 b = 57.514 β = 95.183 c = 122.379 γ = 90
Symmetry Space Group I 1 2 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 2020-07-09 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) 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 1.57 46.08 94 0.046 0.99 9.4 2.4 70014
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 1.57 1.66 0.55 0.7
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 1.573 37.778 70008 3673 94.034 0.184 0.183 0.1913 0.2095 0.2155 27.196
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] 0.061 -0.002 0.051 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.758 r_dihedral_angle_4_deg 20.024 r_dihedral_angle_3_deg 12.73 r_dihedral_angle_1_deg 6.289 r_lrange_it 6.225 r_lrange_other 6.201 r_scangle_it 5.225 r_scangle_other 5.225 r_scbond_it 3.524 r_scbond_other 3.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.758 r_dihedral_angle_4_deg 20.024 r_dihedral_angle_3_deg 12.73 r_dihedral_angle_1_deg 6.289 r_lrange_it 6.225 r_lrange_other 6.201 r_scangle_it 5.225 r_scangle_other 5.225 r_scbond_it 3.524 r_scbond_other 3.523 r_mcangle_it 3.184 r_mcangle_other 3.183 r_mcbond_it 2.275 r_mcbond_other 2.275 r_angle_refined_deg 1.702 r_angle_other_deg 1.511 r_symmetry_nbd_refined 0.291 r_nbd_other 0.225 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.083 r_chiral_restr_other 0.053 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3974 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing