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Crystal structure of the archaeosine synthase QueF-Like in the apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 17-19% PEG3350, 0.15 M potassium thiocyanate, and 0.05% sodium azide.
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.21 α = 90 b = 124.995 β = 112.27 c = 74.404 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 CCD ADSC QUANTUM 315r 2015-11-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97607 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.94 69 99.8 0.049 8.1 7.4 77458
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 1.94 1.98 99.8 0.685 1.8 7.3 4850
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 5JYX 1.94 69 73364 3886 99 0.1589 0.1546 0.1665 0.2385 0.2423 RANDOM 35.243
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] -1.37 -0.31 0.47 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_sphericity_free 27.436 r_dihedral_angle_4_deg 16.548 r_dihedral_angle_3_deg 15.921 r_sphericity_bonded 11.835 r_dihedral_angle_1_deg 6.568 r_rigid_bond_restr 5.447 r_mcangle_it 4.748 r_mcbond_it 4.253 r_mcbond_other 4.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.899 r_sphericity_free 27.436 r_dihedral_angle_4_deg 16.548 r_dihedral_angle_3_deg 15.921 r_sphericity_bonded 11.835 r_dihedral_angle_1_deg 6.568 r_rigid_bond_restr 5.447 r_mcangle_it 4.748 r_mcbond_it 4.253 r_mcbond_other 4.131 r_angle_refined_deg 2.247 r_angle_other_deg 1.105 r_chiral_restr 0.126 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7811 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing