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Crystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) wt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2%(v/v) Tacsimate pH 8.0, 16% w/v Polyethylene glycol 3350, 100mM Tris pH 8.5, 16% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.971 α = 98.14 b = 109.429 β = 98.18 c = 153.854 γ = 89.97
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS PILATUS3 6M 2020-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97942 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.53 50 91.9 0.186 0.22 0.115 2.8 3.5 62046
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.53 3.59 88.9 0.786 0.938 0.507 0.968 3.2
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 2AJT 3.53 49.74 58899 3146 91.56 0.2273 0.2217 0.2179 0.3321 0.3207 RANDOM 110.908
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] -0.17 -0.41 -0.38 0.29 -0.61 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_dihedral_angle_3_deg 18.788 r_dihedral_angle_4_deg 14.814 r_dihedral_angle_1_deg 6.764 r_angle_refined_deg 1.387 r_angle_other_deg 1.121 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_dihedral_angle_3_deg 18.788 r_dihedral_angle_4_deg 14.814 r_dihedral_angle_1_deg 6.764 r_angle_refined_deg 1.387 r_angle_other_deg 1.121 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47675 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing