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Crystal Structure of TorA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 60% PEG 1000, 150 mM di-sodium DL-malate, pH 5.0, 4 mM sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.85 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.662 α = 90 b = 117.467 β = 103.25 c = 100.053 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 PIXEL DECTRIS PILATUS3 S 6M 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.86 47.79 90.88 0.114 0.994 7.45 2.4 159613 22.09
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 1.86 1.91 88.7 0.543 0.609 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.86 47.79 157492 2101 90.84 0.2358 0.2351 0.28875 0.2784 RANDOM 27.921
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] -0.18 -0.23 2.31 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.541 r_long_range_B_refined 8.524 r_long_range_B_other 8.462 r_scangle_other 7.55 r_dihedral_angle_2_deg 7.098 r_dihedral_angle_1_deg 6.706 r_scbond_it 6.018 r_scbond_other 6.018 r_mcangle_it 5.812 r_mcangle_other 5.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.541 r_long_range_B_refined 8.524 r_long_range_B_other 8.462 r_scangle_other 7.55 r_dihedral_angle_2_deg 7.098 r_dihedral_angle_1_deg 6.706 r_scbond_it 6.018 r_scbond_other 6.018 r_mcangle_it 5.812 r_mcangle_other 5.812 r_mcbond_it 4.837 r_mcbond_other 4.833 r_angle_refined_deg 1.116 r_angle_other_deg 0.421 r_chiral_restr 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12507 Nucleic Acid Atoms Solvent Atoms 1544 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction XSCALE data scaling PHASER phasing