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Aquifex aeolicus TsaD-TsaB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YDU Crystal structure other Other AF-A0A7C5Q8I2-F1-model_v4 Alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 9 mg/ml TsaD-TsaB, 0.1 M MES pH 6.5, 30 % PEG 300, 200 mM NaC
Crystal Properties Matthews coefficient Solvent content 3.01 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.719 α = 90 b = 97.719 β = 90 c = 132.204 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 150 PIXEL RIGAKU HyPix-6000HE CMF 2021-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 30.64 99.9 0.103 0.998 30.87 24.5 48654 23.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 0.892
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2 30.52 1.33 48377 2434 97.03 0.219 0.2164 0.2204 0.2669 0.2716 RANDOM 30.65
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.9227 f_angle_d 0.9074 f_chiral_restr 0.057 f_plane_restr 0.008 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4134 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling Coot model building MOLREP phasing