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Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ITB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 MiaE:20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl
reservoir solution: 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8
frozen under 140 bar of krypton
Krypton atoms were located in anomalous map
Crystal Properties Matthews coefficient Solvent content 2.71 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.622 α = 90 b = 52.3 β = 90.74 c = 79.407 γ = 90
Symmetry Space Group C 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 PILATUS3 S 6M 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8610 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.15 80 94.6 0.076 0.99 15.7 6.1 25240 1.4 48.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.28 72.8 0.095 0.69 1.4 3.9
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 (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 THROUGHOUT 2ITB 2.15 79.4 23939 1290 94.61 0.1828 0.1796 0.1888 0.2439 0.2462 RANDOM 48.887
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] -2.27 -1.51 0.92 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_3_deg 17.038 r_dihedral_angle_4_deg 17.003 r_dihedral_angle_1_deg 5.489 r_angle_refined_deg 1.435 r_angle_other_deg 0.977 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_3_deg 17.038 r_dihedral_angle_4_deg 17.003 r_dihedral_angle_1_deg 5.489 r_angle_refined_deg 1.435 r_angle_other_deg 0.977 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3131 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing