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Crystal structure of monooxygenase RutA complexed with Uracil under atmospheric pressure.
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 FMN
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.914 α = 90 b = 87.914 β = 90 c = 97.01 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 2.01 48.51 98.4 0.99 15.3 5 28857
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.12 0.63
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WAN 2.01 43.996 28828 1369 98.292 0.202 0.1999 0.247 0.2414 48.663
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] 0.239 0.12 0.239 -0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.85 r_dihedral_angle_3_deg 16.618 r_dihedral_angle_4_deg 15.349 r_lrange_it 9.222 r_scangle_it 7.759 r_dihedral_angle_1_deg 7.16 r_scbond_it 5.578 r_mcangle_it 5.352 r_mcbond_it 4.155 r_angle_refined_deg 1.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.85 r_dihedral_angle_3_deg 16.618 r_dihedral_angle_4_deg 15.349 r_lrange_it 9.222 r_scangle_it 7.759 r_dihedral_angle_1_deg 7.16 r_scbond_it 5.578 r_mcangle_it 5.352 r_mcbond_it 4.155 r_angle_refined_deg 1.672 r_nbtor_refined 0.318 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.183 r_chiral_restr 0.121 r_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_refined 0.107 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2618 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing