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Crystal structure of thermostable omega transaminase 6-fold mutant from Pseudomonas jessenii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 Succinic acid
Crystal Properties Matthews coefficient Solvent content 2.95 58.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.924 α = 90 b = 98.924 β = 90 c = 120.276 γ = 90
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 EIGER X 4M 2018-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.85 45.79 100 0.069 0.075 0.03 0.999 13 5.9 98464
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 1.85 1.88 100 1.208 1.323 0.534 0.569 6.1
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 FOURIER SYNTHESIS THROUGHOUT 6G4B 1.85 45.74 93393 5035 99.97 0.1577 0.1562 0.1697 0.1867 0.1952 RANDOM 30.011
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] 0.15 0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.974 r_dihedral_angle_4_deg 15.877 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 6.771 r_angle_refined_deg 1.439 r_angle_other_deg 1.336 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.974 r_dihedral_angle_4_deg 15.877 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_1_deg 6.771 r_angle_refined_deg 1.439 r_angle_other_deg 1.336 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6943 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC phasing Aimless data scaling PDB_EXTRACT data extraction XDS data reduction