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FAD-dependent monooxygenase from Stenotrophomonas maltophilia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 12% (w/v) PEG 8000, 24% (v/v) ethylene glycol, 60 mM sodium nitrate, 60 mM disodium hydrogen phosphate, 60 mM ammonium sulfate, 100 mM MES/imidazole pH 6.5, 4% acetone
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.932 α = 90 b = 160.535 β = 95.914 c = 95.563 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 PILATUS 6M 2021-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9180 BESSY 14.1
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 1.95 48.26 85.3 0.138 0.156 0.07 0.997 8.6 4.8 98291 -3.7 39
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 1.95 2.01 48.5 1.531 1.702 0.729 0.378 1.1 5.2
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6N04 1.95 48.26 98291 5781 85.3 0.202 0.2022 0.2002 0.2078 0.241 0.215 Random selection 28.9
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] 0.027 -0.047 0.1 -0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.308 r_dihedral_angle_4_deg 19.712 r_dihedral_angle_3_deg 14.848 r_lrange_it 7.862 r_lrange_other 7.799 r_dihedral_angle_1_deg 6.674 r_scangle_it 5.136 r_scangle_other 5.136 r_mcangle_it 4.384 r_mcangle_other 4.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.308 r_dihedral_angle_4_deg 19.712 r_dihedral_angle_3_deg 14.848 r_lrange_it 7.862 r_lrange_other 7.799 r_dihedral_angle_1_deg 6.674 r_scangle_it 5.136 r_scangle_other 5.136 r_mcangle_it 4.384 r_mcangle_other 4.375 r_scbond_it 3.189 r_scbond_other 3.189 r_mcbond_other 2.729 r_mcbond_it 2.728 r_angle_refined_deg 1.498 r_angle_other_deg 1.314 r_nbd_other 0.212 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.121 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.074 r_ncsr_local_group_3 0.066 r_ncsr_local_group_6 0.064 r_ncsr_local_group_1 0.063 r_ncsr_local_group_4 0.059 r_ncsr_local_group_5 0.057 r_ncsr_local_group_2 0.056 r_symmetry_xyhbond_nbd_other 0.049 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10327 Nucleic Acid Atoms Solvent Atoms 1111 Heterogen Atoms 276
Software Software Software Name Purpose MxCuBE data collection XDS data reduction Aimless data scaling STARANISO data scaling MoRDa phasing PHASER phasing Coot model building REFMAC refinement