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Crystal structure of monooxygenase RutA complexed with 2,4-dimethoxypyrimidine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 100 mM Bis-Tris pH 6.5, 1900 mM ammonium sulphate, 2-5% MPD (v/v), 1 mM 2,4-Dimethoxypyrimidine
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.136 α = 90 b = 87.136 β = 90 c = 95.541 γ = 120
Symmetry Space Group P 31 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 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 47.77 99.5 0.998 11.2 5 14850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 0.615
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 THROUGHOUT 5WAN 2.501 43.606 14827 678 99.37 0.204 0.2007 0.2008 0.2631 0.2631 68.701
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] -0.556 -0.278 -0.556 1.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 18.766 r_dihedral_angle_3_deg 17.102 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.531 r_nbtor_refined 0.318 r_nbd_refined 0.232 r_symmetry_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.192 r_xyhbond_nbd_refined 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 18.766 r_dihedral_angle_3_deg 17.102 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.531 r_nbtor_refined 0.318 r_nbd_refined 0.232 r_symmetry_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.192 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.111 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2587 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing