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Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M3 mutant).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 293 HEPES 0.1M pH 7.5; Sodium chloride 3.4M
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.497 α = 90 b = 146.497 β = 90 c = 143.776 γ = 120
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 2019-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 95.13 98.6 0.045 0.055 0.03 0.999 11.3 2.8 58749
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 1.75 1.78 98.2 0.897 1.102 0.623 0.401 2.8
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 6GKR 2 95.13 37506 1991 98.51 0.1634 0.1614 0.17 0.2007 0.2076 RANDOM 31.195
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] 0.13 0.06 0.13 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.395 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 7.627 r_angle_refined_deg 2.031 r_angle_other_deg 1.533 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.395 r_dihedral_angle_4_deg 21.774 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 7.627 r_angle_refined_deg 2.031 r_angle_other_deg 1.533 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2481 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction