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Crystal structure of the W60C mutant of the (S)-selective transaminase from Chromobacterium violaceum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 100 mM HEPES pH 7.5, 22.5 % w/v PEG 4000, 350 mM NaCl, 0.1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.01 38.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.221 α = 75.03 b = 62.196 β = 81.31 c = 118.423 γ = 75.3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.00964 MAX II I911-2
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 1.8 50.51 96.5 0.18 0.208 0.105 0.985 13.3 3.9 145405
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 1.8 1.83 95 1.187 1.376 0.694 0.238 3.9
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 4A6T 2 48.28 100404 5299 96.2 0.183 0.1813 0.1896 0.2153 0.2218 RANDOM 20.599
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] 0.03 -0.01 -0.03 -0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.372 r_dihedral_angle_4_deg 18.016 r_dihedral_angle_3_deg 15.531 r_dihedral_angle_1_deg 7.244 r_angle_refined_deg 1.84 r_angle_other_deg 1.453 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.372 r_dihedral_angle_4_deg 18.016 r_dihedral_angle_3_deg 15.531 r_dihedral_angle_1_deg 7.244 r_angle_refined_deg 1.84 r_angle_other_deg 1.453 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14297 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction