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Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 2000 bar using the high pressure freezing method
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 protein : 20 mg/ml in 100 mM HEPES, pH 7.5, 30 mM NaCl
reservoir : 0.5 M CaCl2, 42% PEG 6k, 2 M Tris-Cl pH 8
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.388 α = 90 b = 51.909 β = 90.36 c = 78.978 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 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.770 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 2.5 50 99.3 0.065 0.999 16.5 6.2 16699 2.2 72.2
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 2.5 2.65 97.7 0.79 0.912 2.24 6.01
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 2.5 47.52 15868 829 99.33 0.1849 0.1817 0.1897 0.2446 0.2366 RANDOM 69.561
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] -5.55 -3.97 2.01 3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.742 r_dihedral_angle_4_deg 18.659 r_dihedral_angle_3_deg 17.557 r_dihedral_angle_1_deg 5.816 r_angle_refined_deg 1.443 r_angle_other_deg 1.25 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.742 r_dihedral_angle_4_deg 18.659 r_dihedral_angle_3_deg 17.557 r_dihedral_angle_1_deg 5.816 r_angle_refined_deg 1.443 r_angle_other_deg 1.25 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3155 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing