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Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Ala
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32%PEG 3350, 2% glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.761 α = 106.48 b = 83.653 β = 109.07 c = 87.975 γ = 95.12
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 6M 2017-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 2.2 78.58 92.9 0.084 0.099 0.052 0.996 5.9 3.5 99929
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 2.2 2.24 92.6 0.482 0.569 0.299 0.768 3.4
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 5DDS 2.2 30 94926 4959 92.84 0.2061 0.2036 0.2089 0.2542 0.2559 RANDOM 38.424
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] -0.33 -0.37 0.8 -2.82 -0.38 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.189 r_dihedral_angle_4_deg 20.449 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.664 r_angle_other_deg 1.309 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.189 r_dihedral_angle_4_deg 20.449 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.664 r_angle_other_deg 1.309 r_chiral_restr 0.073 r_bond_refined_d 0.01 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 15798 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 136
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction MOLREP phasing